diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index 82f2a32cb..58b1aaf90 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -18,7 +18,7 @@ jobs: - name: Setup Hugo uses: peaceiris/actions-hugo@v2 with: - hugo-version: 0.79.1 + hugo-version: 0.111.3 extended: true - name: Build diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 38a7cdfa7..f534b5603 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: - name: Setup Hugo uses: peaceiris/actions-hugo@v2 with: - hugo-version: 0.79.1 + hugo-version: 0.111.3 extended: true - name: Build diff --git a/.gitignore b/.gitignore index 981f8b3b9..f89832908 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,6 @@ # Hugo resources/ public/ + +CLAUDE.md +.claude/ \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 000000000..99ff09591 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,55 @@ +# Contributing to the SBOL Standard Website + +This guide is for editors and community members who want to add or update content on [sbolstandard.org](https://sbolstandard.org). You do not need to know Hugo, SCSS, or any programming language — all content is written in plain Markdown with a short block of structured data at the top. + +--- + +## Prerequisites + +- A [GitHub account](https://github.com/join) +- Basic familiarity with editing files on GitHub (or cloning a repo locally) + +Installing Hugo and running the site locally allows you to preview changes before submitting. See the main [README](README.md) for local setup instructions. + +--- + +## How to Submit a Change + +1. **Fork** the repository on GitHub. +2. **Create a branch** for your change (e.g. `add-pysbol-library`). +3. **Edit or add files** following the relevant guide below. +4. **Open a Pull Request** against `master`. An editor will review and merge it. + +If you spot a problem but don't want to fix it yourself, [open an issue](https://github.com/SynBioDex/SbolStandardWebsite/issues/new) instead. + +--- + +## Content Guides + +Each guide below covers one type of content, with step-by-step instructions and a real example from the repo. + +| What you want to add or change | Guide | +|---|---| +| News announcement or event notice | [Announcements](docs/editors/01-announcements.md) | +| Blog post | [Blog Posts](docs/editors/02-blog-post.md) | +| Software library | [Libraries](docs/editors/03-library.md) | +| Application or tool | [Applications](docs/editors/04-application.md) | +| GenAI tool or AI resource | [GenAI Tools](docs/editors/05-genai-tool.md) | +| Image in the Visual Gallery | [Visual Gallery](docs/editors/06-visual-gallery.md) | +| Person on the Leadership page | [Leadership](docs/editors/07-leadership.md) | +| Publication | [Publications](docs/editors/08-publication.md) | + +--- + +## General Rules + +- **Never put HTML, CSS, or JavaScript inside Markdown files.** All content files should contain only front matter (the `---` block at the top) and plain Markdown text. Styling and layout are handled by the templates. +- **Follow the folder structure exactly.** Each content type lives in a specific place; the guides show you where. +- **Use the existing entries as your template.** Every guide links to a real example in the repo. +- **Images go in the same folder as the content file** — not in `static/` or anywhere else. + +--- + +## Questions + +Ask on [Slack](https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg) or open a GitHub issue. diff --git a/README.md b/README.md index 1bcb9f36e..313b4b09f 100644 --- a/README.md +++ b/README.md @@ -18,32 +18,7 @@ Feel free to contribute by making a Pull Request. One of the SBOL Editors will r You can also contribute by [creating an issue](https://github.com/SynBioDex/SbolStandardWebsite/issues/new/choose). - -### Adding a Publication - -To add a publication, create a new directory within [`content/publication`](https://github.com/SynBioDex/SbolStandardWebsite/tree/master/content/publication), and add two files: - -* `cite.bib`, containing a citation [in BibTeX format](https://en.wikipedia.org/wiki/BibTeX) -* `index.md`, a markdown file containing details of the paper in a YAML metadata block - -You can use one of the existing publications as a template. - - -### Adding a Tool - -To add a software application or tool, create a new directory within [`content/applications`](https://github.com/SynBioDex/SbolStandardWebsite/tree/master/content/applications), and add an `index.md` file containing a description of the tool with details in a YAML metadata block. - - -### Adding a community member - -To add a community member to the list on the [community page](https://sbolstandard.org/community/), edit the file [`contents/community/_index.md`](https://github.com/SynBioDex/SbolStandardWebsite/blob/master/content/community/_index.md) - - -### Adding a community event - -To add a community event to the list on the [Community Meetings page](https://sbolstandard.org/community-meetings/), edit the file [`content/community-meetings/_index.md`](https://github.com/SynBioDex/SbolStandardWebsite/blob/master/content/community-meetings/_index.md) - -Materials for community events (such as slides or example files) are stored in the separate [SynBioDex/Community-Media repository](https://github.com/SynBioDex/Community-Media) +Please check the [Contributing guide](CONTRIBUTING.md) for more information. ## Building the site locally diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index fb50eecfa..1bf22a7d8 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -1,6 +1,1050 @@ - $sbol-green: #8cc63f; .universal-wrapper{ text-align: justify; } + +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-Regular.woff2') format('woff2'); + font-weight: 400; + font-style: normal; + font-display: swap; +} +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-Italic.woff2') format('woff2'); + font-weight: 400; + font-style: italic; + font-display: swap; +} +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-Light.woff2') format('woff2'); + font-weight: 300; + font-style: normal; + font-display: swap; +} +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-LightItalic.woff2') format('woff2'); + font-weight: 300; + font-style: italic; + font-display: swap; +} +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-Bold.woff2') format('woff2'); + font-weight: 700; + font-style: normal; + font-display: swap; +} +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-BoldItalic.woff2') format('woff2'); + font-weight: 700; + font-style: italic; + font-display: swap; +} +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-Heavy.woff2') format('woff2'); + font-weight: 900; + font-style: normal; + font-display: swap; +} +@font-face { + font-family: 'Nacelle'; + src: url('/fonts/Nacelle-HeavyItalic.woff2') format('woff2'); + font-weight: 900; + font-style: italic; + font-display: swap; +} + +body { + font-family: 'Nacelle', Arial, Helvetica, sans-serif; +} + +/* Make all text use Nacelle */ +h1, h2, h3, h4, h5, h6, +.navbar, .navbar-brand, .nav-link, .dropdown-item { + font-family: 'Nacelle', Arial, Helvetica, sans-serif !important; +} + +/* Optional, keep font weight consistent in headings */ +h1, h2 { font-weight: 700; } +h3, h4 { font-weight: 400; } + +// ── Footer links ───────────────────────────────────────────────────────────── + +.footer-links { + display: flex; + flex-wrap: wrap; + justify-content: center; + gap: 0.4rem 1.75rem; + margin-bottom: 0.5rem; + + a { + color: #888; + text-decoration: none; + font-size: 0.82rem; + font-weight: 600; + letter-spacing: 0.03em; + text-transform: uppercase; + + &:hover { color: $sbol-green; } + } +} + +// ── Glyph grid ─────────────────────────────────────────────────────────────── + +.glyph-group-title { + font-size: 1.3rem; + font-weight: 700; + color: #2b2b2b; + margin: 2.5rem 0 1rem; + padding-bottom: 0.4rem; + border-bottom: 2px solid $sbol-green; +} + +.glyph-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(110px, 1fr)); + gap: 1rem; + margin-top: 2rem; +} + +.glyph-card { + display: flex; + flex-direction: column; + align-items: center; + background: #f8f8f8; + border: 1px solid #eee; + border-radius: 8px; + padding: 1.25rem 0.75rem 0.75rem; + text-decoration: none; + color: inherit; + transition: box-shadow 0.2s ease, transform 0.2s ease; + + &:hover { + box-shadow: 0 4px 16px rgba(0, 0, 0, 0.1); + transform: translateY(-2px); + text-decoration: none; + color: inherit; + } + + img { + width: 64px; + height: 64px; + object-fit: contain; + } + + span { + font-size: 0.7rem; + text-align: center; + color: #666; + margin-top: 0.6rem; + text-transform: capitalize; + line-height: 1.3; + } +} + +// ── Blog list page ──────────────────────────────────────────────────────────── + +.bl-hero { + background: linear-gradient(135deg, #f0f7e8 0%, #e8f4d9 100%); + padding: 3.5rem 1.5rem; + text-align: center; +} + +.bl-hero-inner { + max-width: 660px; + margin: 0 auto; +} + +.bl-hero-label { + display: inline-block; + background: $sbol-green; + color: #fff; + font-size: 0.72rem; + font-weight: 700; + letter-spacing: 0.1em; + text-transform: uppercase; + padding: 0.25rem 0.85rem; + border-radius: 2rem; + margin-bottom: 1.25rem; +} + +.bl-hero-title { + color: #1a1a1a; + font-size: 2.4rem; + font-weight: 800; + line-height: 1.2; + margin-bottom: 0.75rem; +} + +.bl-hero-sub { + color: #555; + font-size: 1.05rem; + line-height: 1.65; + margin: 0; +} + +.bl-wrapper { + padding-top: 3rem; + padding-bottom: 5rem; +} + +// Tag pills (shared by lead and cards) +.bl-tags { + display: flex; + flex-wrap: wrap; + gap: 0.4rem; + margin-bottom: 0.8rem; +} + +.bl-tag { + background: rgba(140, 198, 63, 0.13); + color: #5a8a1a; + font-size: 0.7rem; + font-weight: 700; + letter-spacing: 0.06em; + text-transform: uppercase; + padding: 0.2rem 0.6rem; + border-radius: 2rem; +} + +// Read more / CTA link +.bl-cta { + display: inline-block; + font-size: 0.88rem; + font-weight: 700; + color: $sbol-green; + margin-top: 0.25rem; + text-decoration: none; +} + +// ── Lead / featured post ────────────────────────────────────────────────────── + +.bl-lead { + display: grid; + grid-template-columns: 1fr 1fr; + gap: 0; + background: #fff; + border-radius: 12px; + box-shadow: 0 4px 28px rgba(0, 0, 0, 0.09); + overflow: hidden; + margin-bottom: 3.5rem; + text-decoration: none; + color: inherit; + transition: box-shadow 0.22s ease, transform 0.22s ease; + + &:hover { + box-shadow: 0 10px 40px rgba(0, 0, 0, 0.14); + transform: translateY(-3px); + text-decoration: none; + color: inherit; + + .bl-lead-img img { transform: scale(1.04); } + .bl-cta { text-decoration: underline; } + } +} + +.bl-lead-img { + overflow: hidden; + min-height: 340px; + + img { + width: 100%; + height: 100%; + object-fit: cover; + display: block; + transition: transform 0.38s ease; + } +} + +.bl-lead--no-img { + grid-template-columns: 1fr; + + .bl-lead-body { + max-width: 680px; + } +} + +.bl-lead-body { + padding: 2.75rem 2.5rem; + display: flex; + flex-direction: column; + justify-content: center; +} + +.bl-lead-title { + font-size: 1.7rem; + font-weight: 700; + line-height: 1.25; + color: #1e1e1e; + margin: 0 0 0.4rem; +} + +.bl-lead-date { + font-size: 0.8rem; + color: #bbb; + margin-bottom: 0.85rem; +} + +.bl-lead-summary { + font-size: 1rem; + color: #555; + line-height: 1.7; + margin-bottom: 1.25rem; +} + +// ── Card grid ───────────────────────────────────────────────────────────────── + +.bl-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(290px, 1fr)); + gap: 2rem; +} + +.bl-card { + background: #fff; + border-radius: 10px; + box-shadow: 0 2px 16px rgba(0, 0, 0, 0.07); + overflow: hidden; + display: flex; + flex-direction: column; + text-decoration: none; + color: inherit; + transition: box-shadow 0.2s ease, transform 0.2s ease; + + &:hover { + box-shadow: 0 8px 32px rgba(0, 0, 0, 0.13); + transform: translateY(-4px); + text-decoration: none; + color: inherit; + + .bl-card-img img { transform: scale(1.05); } + .bl-cta { text-decoration: underline; } + } +} + +.bl-card-img { + height: 200px; + overflow: hidden; + + img { + width: 100%; + height: 100%; + object-fit: cover; + display: block; + transition: transform 0.38s ease; + } +} + +.bl-card-body { + padding: 1.5rem; + display: flex; + flex-direction: column; + flex: 1; +} + +.bl-card-title { + font-size: 1.05rem; + font-weight: 700; + line-height: 1.3; + color: #1e1e1e; + margin: 0.25rem 0 0.3rem; +} + +.bl-card-date { + font-size: 0.76rem; + color: #bbb; + margin-bottom: 0.6rem; +} + +.bl-card-summary { + font-size: 0.88rem; + color: #666; + line-height: 1.65; + flex: 1; + margin-bottom: 0.9rem; +} + +// ── Responsive ──────────────────────────────────────────────────────────────── + +@media (max-width: 860px) { + .bl-lead { + grid-template-columns: 1fr; + } + + .bl-lead-img { + min-height: 220px; + } + + .bl-lead-placeholder { + min-height: 220px; + } + + .bl-hero-title { + font-size: 2.4rem; + } +} + +@media (max-width: 560px) { + .bl-hero-title { font-size: 2rem; } + .bl-lead-body { padding: 1.75rem; } + .bl-grid { grid-template-columns: 1fr; } +} + +// ── Applications / Tools page ───────────────────────────────────────────────── + +.app-hero { + background: linear-gradient(135deg, #f0f7e8 0%, #e8f4d9 100%); + padding: 3.5rem 1.5rem; + text-align: center; +} + +.app-hero-inner { + max-width: 700px; + margin: 0 auto; +} + +.app-hero-label { + display: inline-block; + background: $sbol-green; + color: #fff; + font-size: 0.72rem; + font-weight: 700; + letter-spacing: 0.1em; + text-transform: uppercase; + padding: 0.25rem 0.85rem; + border-radius: 2rem; + margin-bottom: 1.25rem; +} + +.app-hero-title { + color: #1a1a1a; + font-size: 2.4rem; + font-weight: 800; + line-height: 1.2; + margin-bottom: 0.75rem; +} + +.app-hero-sub { + color: #555; + font-size: 1.05rem; + line-height: 1.65; + margin: 0; +} + +.app-wrapper { + padding-top: 2.5rem; + padding-bottom: 5rem; +} + +// ── Filter bar ──────────────────────────────────────────────────────────────── + +.app-filters { + display: flex; + flex-wrap: wrap; + gap: 0.5rem; + margin-bottom: 2rem; +} + +.app-filter-btn { + display: inline-flex; + align-items: center; + gap: 0.4rem; + background: #f4f4f4; + border: 1px solid #e0e0e0; + border-radius: 2rem; + padding: 0.35rem 0.85rem; + font-size: 0.82rem; + font-weight: 600; + color: #555; + cursor: pointer; + transition: background 0.15s ease, border-color 0.15s ease, color 0.15s ease; + + &:hover { + background: rgba(140, 198, 63, 0.12); + border-color: $sbol-green; + color: #3a6010; + } + + &.active { + background: $sbol-green; + border-color: $sbol-green; + color: #fff; + + .app-filter-count { background: rgba(255,255,255,0.25); color: #fff; } + } +} + +.app-filter-count { + display: inline-block; + background: #e0e0e0; + color: #777; + font-size: 0.68rem; + font-weight: 700; + border-radius: 1rem; + padding: 0 0.38rem; + line-height: 1.5; + transition: background 0.15s ease, color 0.15s ease; +} + +// ── Card grid ───────────────────────────────────────────────────────────────── + +.app-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(280px, 1fr)); + gap: 1.5rem; + align-items: start; +} + +.app-card { + background: #fff; + border: 1px solid #e8e8e8; + border-radius: 10px; + padding: 1.4rem 1.5rem; + display: flex; + flex-direction: column; + gap: 0.6rem; + transition: box-shadow 0.18s ease, transform 0.18s ease; + + &:hover { + box-shadow: 0 6px 24px rgba(0, 0, 0, 0.09); + transform: translateY(-2px); + } +} + +.app-card-header { + display: flex; + align-items: center; + justify-content: space-between; + gap: 0.5rem; +} + +.app-card-name { + font-size: 1rem; + font-weight: 700; + color: #1e1e1e; + line-height: 1.3; + text-decoration: none; + + &:hover { color: $sbol-green; text-decoration: none; } +} + +.app-card-link { + color: #bbb; + flex-shrink: 0; + display: flex; + transition: color 0.15s ease; + + &:hover { color: $sbol-green; } +} + +.app-card-summary { + font-size: 0.85rem; + color: #666; + line-height: 1.6; + margin: 0; + flex: 1; +} + +.app-card-tags { + display: flex; + flex-wrap: wrap; + gap: 0.35rem; + margin-top: 0.25rem; +} + +// Tag colors per category +.app-tag { + display: inline-block; + font-size: 0.65rem; + font-weight: 700; + letter-spacing: 0.06em; + text-transform: uppercase; + padding: 0.18rem 0.55rem; + border-radius: 2rem; + border: 1px solid transparent; +} + +.app-tag--design { background: rgba(52, 152, 219, 0.1); border-color: rgba(52, 152, 219, 0.35); color: #1a6fa0; } +.app-tag--simulation { background: rgba(155, 89, 182, 0.1); border-color: rgba(155, 89, 182, 0.35); color: #6c3483; } +.app-tag--visualization{ background: rgba(230, 126, 34, 0.1); border-color: rgba(230, 126, 34, 0.35); color: #a04000; } +.app-tag--repository { background: rgba(140, 198, 63, 0.12); border-color: rgba(140, 198, 63, 0.4); color: #4a7a10; } +.app-tag--converter { background: rgba(52, 73, 94, 0.1); border-color: rgba(52, 73, 94, 0.3); color: #34495e; } + +// ── CTA card ───────────────────────────────────────────────────────────────── + +.app-card--cta { + border: 2px dashed #d0d0d0; + background: #fafafa; + align-items: center; + text-align: center; + justify-content: center; + gap: 0.75rem; + min-height: 180px; + + &:hover { + border-color: $sbol-green; + box-shadow: none; + transform: none; + } +} + +.app-cta-icon { + color: #ccc; + line-height: 1; +} + +.app-cta-title { + font-size: 1rem; + font-weight: 700; + color: #333; + margin: 0; +} + +.app-cta-body { + font-size: 0.84rem; + color: #888; + line-height: 1.5; + margin: 0; +} + +// ── Deprecated / Legacy section ─────────────────────────────────────────────── + +.app-deprecated { + margin-top: 4rem; + padding-top: 2.5rem; + border-top: 1px solid #e8e8e8; +} + +.app-deprecated-heading { + font-size: 1.25rem; + font-weight: 700; + color: #555; + margin-bottom: 0.4rem; +} + +.app-deprecated-sub { + font-size: 0.88rem; + color: #aaa; + margin-bottom: 1.5rem; +} + +.app-deprecated-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(260px, 1fr)); + gap: 1rem; +} + +.app-dep-card { + background: #f9f9f9; + border: 1px solid #ececec; + border-radius: 8px; + padding: 1rem 1.1rem; + display: flex; + flex-direction: column; + gap: 0.4rem; + opacity: 0.8; +} + +.app-dep-name { + font-size: 0.95rem; + font-weight: 700; + color: #555; + + a { color: inherit; text-decoration: none; &:hover { color: $sbol-green; } } +} + +.app-dep-badge { + display: inline-block; + background: #eee; + color: #999; + font-size: 0.62rem; + font-weight: 700; + letter-spacing: 0.06em; + text-transform: uppercase; + padding: 0.1rem 0.45rem; + border-radius: 2rem; + align-self: flex-start; +} + +.app-dep-summary { + font-size: 0.82rem; + color: #888; + line-height: 1.55; + margin: 0; +} + +// ── Responsive ──────────────────────────────────────────────────────────────── + +@media (max-width: 860px) { + .app-hero-title { font-size: 2.4rem; } +} + +@media (max-width: 560px) { + .app-hero-title { font-size: 2rem; } + .app-grid { grid-template-columns: 1fr; } + .app-deprecated-grid { grid-template-columns: 1fr; } +} + +// ── Libraries page ──────────────────────────────────────────────────────────── + +.lib-hero { + background: linear-gradient(135deg, #f0f7e8 0%, #e8f4d9 100%); + padding: 3.5rem 1.5rem; + text-align: center; +} + +.lib-hero-inner { + max-width: 700px; + margin: 0 auto; +} + +.lib-hero-title { + color: #1a1a1a; + font-size: 2.4rem; + font-weight: 800; + line-height: 1.2; + margin-bottom: 0.75rem; +} + +.lib-hero-sub { + color: #555; + font-size: 1.05rem; + line-height: 1.65; + margin-bottom: 2rem; +} + +.lib-hero-btns { + display: flex; + gap: 0.75rem; + justify-content: center; + flex-wrap: wrap; +} + +.lib-btn-outline-white { + background: transparent; + border: 2px solid rgba(255,255,255,0.5); + color: #fff; + border-radius: 4px; + padding: 0.5rem 1.25rem; + font-size: 0.82rem; + font-weight: 700; + letter-spacing: 0.06em; + text-transform: uppercase; + text-decoration: none; + transition: border-color 0.15s ease, background 0.15s ease; + + &:hover { border-color: #fff; background: rgba(255,255,255,0.08); color: #fff; text-decoration: none; } +} + +// ── Tab bar ─────────────────────────────────────────────────────────────────── + +.lib-tabs-bar { + border-bottom: 2px solid #e8e8e8; + background: #fff; + position: sticky; + top: 0; + z-index: 10; +} + +.lib-tabs-wrap { + display: flex; + gap: 0; + padding-top: 0; + padding-bottom: 0; +} + +.lib-tab { + background: none; + border: none; + border-bottom: 3px solid transparent; + padding: 1rem 1.5rem; + font-size: 0.88rem; + font-weight: 700; + color: #888; + cursor: pointer; + margin-bottom: -2px; + transition: color 0.15s ease, border-color 0.15s ease; + font-family: 'Nacelle', Arial, Helvetica, sans-serif; + + &:hover { color: #333; } + + &.active { + color: $sbol-green; + border-bottom-color: $sbol-green; + } +} + +// ── Panel ───────────────────────────────────────────────────────────────────── + +.lib-wrapper { + padding-top: 3rem; + padding-bottom: 5rem; +} + +.lib-panel--hidden { + display: none; +} + +// ── Section header ──────────────────────────────────────────────────────────── + +.lib-section-header { + display: flex; + align-items: flex-start; + justify-content: space-between; + gap: 1rem; + margin-bottom: 1.75rem; + + &--spaced { margin-top: 3rem; } +} + +.lib-section-title { + font-size: 1.5rem; + font-weight: 700; + color: #1e1e1e; + margin: 0 0 0.3rem; +} + +.lib-section-sub { + font-size: 0.88rem; + color: #888; + margin: 0; +} + +.lib-badge { + display: inline-block; + font-size: 0.65rem; + font-weight: 700; + letter-spacing: 0.08em; + text-transform: uppercase; + padding: 0.25rem 0.7rem; + border-radius: 2rem; + white-space: nowrap; + flex-shrink: 0; + margin-top: 0.2rem; +} + +.lib-badge--active { + background: rgba(140, 198, 63, 0.15); + color: #4a7a10; + border: 1px solid rgba(140, 198, 63, 0.4); +} + +// ── Primary Library cards (large, 2-col) ────────────────────────────────────── + +.lib-primary-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(340px, 1fr)); + gap: 1.5rem; + margin-bottom: 3.5rem; +} + +.lib-primary-card { + background: #fff; + border: 1px solid #e0e0e0; + border-radius: 12px; + padding: 1.75rem 1.75rem 1.5rem; + display: flex; + flex-direction: column; + gap: 0.75rem; + box-shadow: 0 2px 12px rgba(0,0,0,0.05); + transition: box-shadow 0.18s ease, transform 0.18s ease; + + &:hover { + box-shadow: 0 6px 24px rgba(0,0,0,0.1); + transform: translateY(-2px); + } +} + +.lib-primary-card-header { + display: flex; + align-items: center; + justify-content: space-between; +} + +.lib-primary-name { + font-size: 1.15rem; + font-weight: 700; + color: #1e1e1e; +} + +.lib-primary-summary { + font-size: 0.9rem; + color: #555; + line-height: 1.65; + margin: 0; + flex: 1; +} + +.lib-primary-actions { + display: flex; + gap: 0.6rem; + flex-wrap: wrap; + margin-top: 0.25rem; +} + +.lib-btn-dark { + background: #1e1e1e; + color: #fff !important; + border: 1px solid #1e1e1e; + font-size: 0.75rem; + font-weight: 700; + letter-spacing: 0.06em; + text-transform: uppercase; + padding: 0.4rem 0.9rem; + border-radius: 4px; + text-decoration: none; + transition: background 0.15s ease; + + &:hover { background: #333; text-decoration: none; } +} + +.lib-btn-outline { + background: transparent; + color: #333 !important; + border: 1px solid #ccc; + font-size: 0.75rem; + font-weight: 700; + letter-spacing: 0.06em; + text-transform: uppercase; + padding: 0.4rem 0.9rem; + border-radius: 4px; + text-decoration: none; + transition: border-color 0.15s ease, color 0.15s ease; + + &:hover { border-color: $sbol-green; color: $sbol-green !important; text-decoration: none; } +} + +// ── Other Libraries grid ────────────────────────────────────────────────────── + +.lib-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(340px, 1fr)); + gap: 1.5rem; +} + +.lib-card { + background: #fff; + border: 1px solid #e8e8e8; + border-radius: 10px; + padding: 1.25rem 1.35rem; + display: flex; + flex-direction: column; + gap: 0.5rem; + transition: box-shadow 0.18s ease; + + &:hover { box-shadow: 0 4px 16px rgba(0,0,0,0.08); } +} + +.lib-card-header { + display: flex; + align-items: center; + justify-content: space-between; +} + +.lib-card-name { + font-size: 1rem; + font-weight: 700; + color: #1e1e1e; +} + +.lib-card-summary { + font-size: 0.84rem; + color: #666; + line-height: 1.6; + margin: 0; + flex: 1; +} + +.lib-card-actions { + margin-top: 0.25rem; +} + +.lib-cta { + font-size: 0.82rem; + font-weight: 700; + color: $sbol-green; + text-decoration: none; + + &:hover { text-decoration: underline; } +} + +// ── External link icon ──────────────────────────────────────────────────────── + +.lib-ext-link { + color: #bbb; + display: flex; + transition: color 0.15s ease; + + &:hover { color: $sbol-green; } +} + +// ── Developer Resources ─────────────────────────────────────────────────────── + +.lib-devres { + margin-top: 3.5rem; + padding-top: 3rem; + border-top: 1px solid #e8e8e8; +} + +.lib-devres-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(300px, 1fr)); + gap: 1.5rem; + margin-top: 1.5rem; +} + +.lib-devres-card { + background: #f8f8f8; + border: 1px solid #ececec; + border-radius: 10px; + padding: 1.5rem; + display: flex; + flex-direction: column; + gap: 0.5rem; +} + +.lib-devres-name { + font-size: 1rem; + font-weight: 700; + color: #1e1e1e; + margin: 0; +} + +.lib-devres-desc { + font-size: 0.86rem; + color: #666; + line-height: 1.6; + margin: 0; + flex: 1; +} + +.lib-devres-cta { + font-size: 0.82rem; + font-weight: 700; + color: $sbol-green; + text-decoration: none; + margin-top: 0.25rem; + + &:hover { text-decoration: underline; } +} + +// ── Responsive ──────────────────────────────────────────────────────────────── + +@media (max-width: 860px) { + .lib-hero-title { font-size: 2.4rem; } + .lib-section-header { flex-direction: column; align-items: flex-start; } +} + +@media (max-width: 560px) { + .lib-hero-title { font-size: 2rem; } + .lib-primary-grid { grid-template-columns: 1fr; } + .lib-grid { grid-template-columns: 1fr; } + .lib-devres-grid { grid-template-columns: 1fr; } +} \ No newline at end of file diff --git a/config/_default/menus.toml b/config/_default/menus.toml index c028478e3..d891fe681 100644 --- a/config/_default/menus.toml +++ b/config/_default/menus.toml @@ -3,10 +3,6 @@ # desired widget in your `content/home/` folder. # The weight parameter defines the order that the links will appear in. -[[main]] - name = "Home" - url = "#about" - weight = 10 [[main]] name = "SBOL Data Model" @@ -26,30 +22,12 @@ weight = 10 parent = "dom-id" -[[main]] - name = "Libraries" - url = "/libraries" - weight = 15 - parent = "dom-id" - [[main]] name = "SBOL Ontology" url = "/ontology" weight = 20 parent = "dom-id" -[[main]] - name = "Converter" - url = "https://converter.sbolstandard.org/" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "https://validator.sbolstandard.org/" - weight = 30 - parent = "dom-id" - [[main]] name = "Examples" url = "/DataModel-Examples" @@ -86,28 +64,91 @@ weight = 20 parent = "visual-id" +#[[main]] +# name = "Examples from papers" +# url = "/visual-examples" +# weight = 25 +# parent = "visual-id" + [[main]] - name = "Examples from papers" - url = "/visual-examples" - weight = 25 + name = "Gallery" + url = "/visual-gallery" + weight = 27 parent = "visual-id" [[main]] - name = "Examples from specification" - url = "/visual-spec-examples" - weight = 25 + name = "10 Years of SBOL Visual" + url = "/sbolv-10-years" + weight = 30 parent = "visual-id" - + +[[main]] + name = "Ecosystem" + url = "/ecosystem" + weight = 30 + identifier = "ecosystem-id" + +[[main]] + name = "Libraries" + url = "/libraries" + weight = 5 + parent = "ecosystem-id" + [[main]] name = "Applications" - url = "#applications" + url = "/applications" + weight = 10 + parent = "ecosystem-id" + + [[main]] + name = "Converter" + url = "https://converter.sbolstandard.org/" + weight = 15 + parent = "ecosystem-id" + +[[main]] + name = "Validator" + url = "https://validator.sbolstandard.org/" + weight = 20 + parent = "ecosystem-id" + +[[main]] + name = "GitHub" + url = "https://github.com/SynBioDex/" + weight = 25 + parent = "ecosystem-id" + +[[main]] + name = "GenAI Tools" + url = "/genai-tools" weight = 30 + parent = "ecosystem-id" [[main]] name = "Publications" url = "/publication" weight = 40 +[[main]] + name = "News" + url = "/news" + weight = 45 + identifier = "news-id" + +[[main]] + name = "Announcements" + url = "/post" + weight = 5 + parent = "news-id" + +[[main]] + name = "Blog" + url = "/blog" + weight = 10 + parent = "news-id" + + + [[main]] name = "Community" url = "/community" @@ -115,22 +156,24 @@ identifier = "community-id" [[main]] - name = "About" - url = "/community" + name = "Leadership" + url = "/community-leadership" weight = 5 parent = "community-id" [[main]] - name = "Meetings" + name = "Meetings & Outreach" url = "/community-meetings" - weight = 10 + weight = 12 parent = "community-id" -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" +#[[main]] +# name = "Outreach" +# url = "/community-outreach" +# weight = 15 +# parent = "community-id" + + [[main]] name = "Governance" @@ -138,62 +181,46 @@ weight = 20 parent = "community-id" +#[[main]] +# name = "SBOL Industrial Consortium" +# url = "/sbol-industrial" +# weight = 25 +# parent = "community-id" + [[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 + name = "Sponsor SBOL" + url = "/sponsor-sbol" + weight = 30 parent = "community-id" -[[main]] - name = "Contact" - url = "/contact" - weight = 55 +# Footer Links -[[main]] - name = "Help" - url = "/faq" - weight = 60 - identifier = "help-id" +[[footer]] + name = "Contact Us" + url = "/contact" + weight = 10 -[[main]] +[[footer]] name = "FAQ" url = "/faq" - weight = 62 - parent = "help-id" + weight = 20 -[[main]] - name = "StackExchange" +[[footer]] + name = "Stack Exchange" url = "https://bioinformatics.stackexchange.com/questions/tagged/sbol" - weight = 64 - parent = "help-id" - -[[main]] - name = "About" - url = "/about" - weight = 70 - identifier = "about-id" + weight = 30 -[[main]] +[[footer]] name = "View Source" url = "https://github.com/SynBioDex/SbolStandardWebsite" - weight = 75 - parent = "about-id" + weight = 40 -[[main]] +[[footer]] name = "Community Media" url = "https://github.com/SynBioDex/Community-Media" - weight = 80 - parent = "about-id" + weight = 50 -[[main]] +[[footer]] name = "Report an Issue" url = "https://github.com/SynBioDex/SbolStandardWebsite/issues" - weight = 85 - parent = "about-id" - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 + weight = 60 diff --git a/config/_default/params.toml b/config/_default/params.toml index d44bde411..0600af776 100644 --- a/config/_default/params.toml +++ b/config/_default/params.toml @@ -22,7 +22,7 @@ day_night = false # Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ # Browse built-in font sets in `themes/academic/data/fonts/` # Browse user installed font sets in `data/fonts/` -font = "" +font = "nacelle" # Choose a font size. # Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) @@ -281,7 +281,7 @@ plugins_js = [] ## Marketing ############################ [marketing] - google_analytics = "" + google_analytics = "G-TPYBMPPQZ1" google_tag_manager = "" ############################ diff --git a/content/applications/_index.md b/content/applications/_index.md index 381c1e260..207efbecc 100644 --- a/content/applications/_index.md +++ b/content/applications/_index.md @@ -1,21 +1,5 @@ --- title: Applications - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 5 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" +subtitle: Community-contributed software supporting SBOL Core and SBOL Visual, enabling you to design, simulate, visualize, and share genetic designs. +submit_url: https://forms.gle/1UmX3CeCb973G9jE9 --- - -If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks. Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs. - -{{< figure width="600px" library="true" src="SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -If you would like us to feature your application here, please fill out this [survey](https://docs.google.com/forms/d/e/1FAIpQLScOTJLCoTniVPrMh88eg74Eaubh1bFMjncbyG6yt8q4cFLQ-Q/viewform). diff --git a/content/applications/boost/index.md b/content/applications/boost/index.md index c66928dba..d38dbc97b 100644 --- a/content/applications/boost/index.md +++ b/content/applications/boost/index.md @@ -1,7 +1,7 @@ --- title: BOOST summary: A platform of tools to design DNA sequences for manufacturing -tags: ["Sequence Design", "SBOL1 Import", "SBOL1 Export", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design", "Converter"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/cello/index.md b/content/applications/cello/index.md index a9b73caec..3dbd805a5 100644 --- a/content/applications/cello/index.md +++ b/content/applications/cello/index.md @@ -1,7 +1,7 @@ --- title: Cello summary: A tool for Genetic circuit design automation -tags: ["Circuit Design", "Modeling", "SBOL Visual", "SBOL2 Export"] +tags: ["Design", "Simulation"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/device-editor/index.md b/content/applications/device-editor/index.md index 80690c86b..12c942b24 100644 --- a/content/applications/device-editor/index.md +++ b/content/applications/device-editor/index.md @@ -1,7 +1,7 @@ --- title: Device Editor summary: Visual biocad canvas for specifying combinatorial DNA constructs for fabrication -tags: ["Knowledge Management", "Sequence Design", "Circuit Design", "Visualization", "SBOL Visual", "SBOL1 Import", "SBOL1 Export"] +tags: ["Design", "Visualization", "Repository"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/dnaplotlib/index.md b/content/applications/dnaplotlib/index.md index b53875377..0483a9805 100644 --- a/content/applications/dnaplotlib/index.md +++ b/content/applications/dnaplotlib/index.md @@ -1,7 +1,7 @@ --- title: DNAplotlib summary: DNAplotlib enables highly customizable visualization of individual genetic constructs and libraries of design variants. It can be thought of in many ways as matplotlib for genetic diagrams. -tags: ["Visualization", "SBOL Visual", "SBOL1 Import", "SBOL1 Export", "SBOL2 Import", "SBOL2 Export"] +tags: ["Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). @@ -12,10 +12,10 @@ image: focal_point: Smart links: -- icon: edge - icon_pack: fab - name: Link - url: http://dnaplotlib.org/ +#- icon: edge +# icon_pack: fab +# name: Link +# url: http://dnaplotlib.org/ - icon: github icon_pack: fab name: Source Code diff --git a/content/applications/eugene/index.md b/content/applications/eugene/index.md index f66cfc076..3bebb20fe 100644 --- a/content/applications/eugene/index.md +++ b/content/applications/eugene/index.md @@ -1,7 +1,7 @@ --- title: Eugene summary: A textual specification language for the rule-based design of synthetic biological systems, devices, parts, and DNA sequences. -tags: ["Sequence Design", "Circuit Design", "Visualization", "SBOL Visual", "SBOL1 Import", "SBOL1 Export", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design", "Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/finch/index.md b/content/applications/finch/index.md index 8b9318033..becda0551 100644 --- a/content/applications/finch/index.md +++ b/content/applications/finch/index.md @@ -1,8 +1,9 @@ --- title: Finch summary: Rule-based generation of constructs -tags: ["Knowledge Management", "Sequence Design", "Circuit Design", "Visualization", "SBOL Visual", "SBOL2 Export"] +tags: ["Design", "Visualization", "Repository"] date: "2020-06-30T00:00:00Z" +active: false # Optional external URL for project (replaces project detail page). external_link: "" diff --git a/content/applications/flapjack/index.md b/content/applications/flapjack/index.md index 4aacf8cbf..f7b8662f1 100644 --- a/content/applications/flapjack/index.md +++ b/content/applications/flapjack/index.md @@ -1,7 +1,7 @@ --- title: Flapjack summary: Flapjack is a data management and analysis app for genetic circuit characterization to store, share, mix, analyze and plot your SynBio data -tags: ["Knowledge management", "Modeling", "Visualization", "SBOL2", "SBOL3"] +tags: ["Simulation", "Visualization", "Repository"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/genegenie/index.md b/content/applications/genegenie/index.md index 1bac1fbdb..e90bdd697 100644 --- a/content/applications/genegenie/index.md +++ b/content/applications/genegenie/index.md @@ -1,7 +1,7 @@ --- title: GeneGenie summary: GeneGenie supports the design and self-assembly of synthetic genes and constructs. -tags: ["Sequence Design", "SBOL1 Export"] +tags: ["Design"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/genetech/index.md b/content/applications/genetech/index.md index 8f0e63d69..460aa28ad 100644 --- a/content/applications/genetech/index.md +++ b/content/applications/genetech/index.md @@ -1,7 +1,7 @@ --- title: GeneTech summary: A tool which allows a user to generate genetic logic circuits only by specifying the logical function desired to be achieved in a living cell. -tags: ["Circuit Design", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/genocad/index.md b/content/applications/genocad/index.md index d6a3de1a3..723bff8e6 100644 --- a/content/applications/genocad/index.md +++ b/content/applications/genocad/index.md @@ -1,8 +1,9 @@ --- title: GenoCAD summary: A rule-based DNA design tool. -tags: ["Knowledge Management", "Sequence Design", "Circuit Design", "SBOL Visual", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design", "Repository"] date: "2020-06-30T00:00:00Z" +active: false # Optional external URL for project (replaces project detail page). external_link: "" diff --git a/content/applications/graphviz/index.md b/content/applications/graphviz/index.md index ea3b4053c..de5da834b 100644 --- a/content/applications/graphviz/index.md +++ b/content/applications/graphviz/index.md @@ -1,7 +1,7 @@ --- title: Graphviz summary: a package of open-source tools initiated by AT&T Labs Research for drawing graphs specified in DOT language scripts. -tags: ["Visualization", "SBOL Visual"] +tags: ["Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/ibiosim/index.md b/content/applications/ibiosim/index.md index c3f1bef7f..328dac936 100644 --- a/content/applications/ibiosim/index.md +++ b/content/applications/ibiosim/index.md @@ -1,7 +1,7 @@ --- title: iBioSim summary: iBioSim has been developed for the modeling, analysis, and design of genetic circuits. -tags: ["Circuit Design", "Modeling", "Visualization", "SBOL Visual", "SBOL1 Import", "SBOL1 Export", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design", "Simulation", "Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/ice/index.md b/content/applications/ice/index.md index c9ef41acb..797549b88 100644 --- a/content/applications/ice/index.md +++ b/content/applications/ice/index.md @@ -1,7 +1,7 @@ --- title: ICE summary: Physical and Informatic repository and associated tools for plant seeds, microbial strains, DNA and protein sequences. -tags: ["Knowledge Management", "Sequence Design", "Visualization", "SBOL Visual", "SBOL2 Import", "SBOL2 Export"] +tags: ["Repository", "Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/j5/index.md b/content/applications/j5/index.md index 0dfc1facf..ba50ca715 100644 --- a/content/applications/j5/index.md +++ b/content/applications/j5/index.md @@ -1,7 +1,7 @@ --- title: j5 summary: DNA assembly design automation -tags: ["Sequence Design", "Modeling", "SBOL Visual", "SBOL1 Import", "SBOL1 Export"] +tags: ["Design", "Simulation"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/mosec/index.md b/content/applications/mosec/index.md index 4484d3ff2..b22b9f525 100644 --- a/content/applications/mosec/index.md +++ b/content/applications/mosec/index.md @@ -1,7 +1,7 @@ --- title: MoSeC summary: Automated derivation of genetic circuit designs from computational models. -tags: ["Sequence Design", "Circuit Design", "Visualization","SBOL1 Export"] +tags: ["Design", "Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/partsandpools/index.md b/content/applications/partsandpools/index.md index 87fa5b494..28d672039 100644 --- a/content/applications/partsandpools/index.md +++ b/content/applications/partsandpools/index.md @@ -1,7 +1,7 @@ --- title: Parts & Pools summary: A graphical, drag and drop design of synthetic gene circuit with Standard Biological Parts. -tags: ["Circuit Design","Modeling"] +tags: ["Design", "Simulation"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/pigeon/index.md b/content/applications/pigeon/index.md index 7edc17256..100dbc443 100644 --- a/content/applications/pigeon/index.md +++ b/content/applications/pigeon/index.md @@ -1,7 +1,7 @@ --- title: Pigeon Visualizer summary: A tool for creating SBOL Visual diagrams from a concise textual representation. -tags: ["Visualization", "SBOL Visual"] +tags: ["Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/pinecone/index.md b/content/applications/pinecone/index.md index 02306679a..a35b04883 100644 --- a/content/applications/pinecone/index.md +++ b/content/applications/pinecone/index.md @@ -1,8 +1,9 @@ --- title: Pinecone summary: Serotiny’s web-based protein design software aimed at researchers doing R&D for therapeutics, materials, as well as those in basic research. -tags: ["Knowledge Management", "Sequence Design", "SBOL Visual", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design", "Repository"] date: "2020-06-30T00:00:00Z" +active: false # Optional external URL for project (replaces project detail page). external_link: "" diff --git a/content/applications/pooldesigner/index.md b/content/applications/pooldesigner/index.md index 5092e01ef..8620dec17 100644 --- a/content/applications/pooldesigner/index.md +++ b/content/applications/pooldesigner/index.md @@ -1,7 +1,7 @@ --- title: Pool Designer summary: Designing Multiplexed Pools for Assembling Library Constructs -tags: ["Sequence Design", "SBOL Visual", "SBOL1 Import", "SBOL2 Import"] +tags: ["Design"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/protobiocompiler/index.md b/content/applications/protobiocompiler/index.md index 35c8d8f41..eeefbd607 100644 --- a/content/applications/protobiocompiler/index.md +++ b/content/applications/protobiocompiler/index.md @@ -1,8 +1,9 @@ --- title: Proto BioCompiler summary: Proto BioCompiler generates optimized genetic regulatory network designs from specifications written in a high-level programming language, producing both SBOL specifications, visualization, and ODE models. -tags: ["Circuit Design", "Modeling", "Visualization", "SBOL Visual"] +tags: ["Design", "Simulation", "Visualization"] date: "2020-06-30T00:00:00Z" +active: false # Optional external URL for project (replaces project detail page). external_link: "" diff --git a/content/applications/sbolcanvas/index.md b/content/applications/sbolcanvas/index.md index 12899af96..3912b658d 100644 --- a/content/applications/sbolcanvas/index.md +++ b/content/applications/sbolcanvas/index.md @@ -1,7 +1,7 @@ --- title: SBOLCanvas summary: A web application for creation and editing of genetic constructs using the SBOL data and visual standard. -tags: ["Knowledge Management", "Visualization", "SBOL Visual", "SBOL1 Import", "SBOL1 Export", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design", "Visualization", "Repository"] date: "2022-06-08T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/sboldesigner/index.md b/content/applications/sboldesigner/index.md index ad381e9bb..f82945f5d 100644 --- a/content/applications/sboldesigner/index.md +++ b/content/applications/sboldesigner/index.md @@ -1,7 +1,7 @@ --- title: SBOLDesigner summary: A simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using SBOL -tags: ["Knowledge Management", "Sequence Design", "Visualization", "SBOL Visual", "SBOL1 Import", "SBOL1 Export", "SBOL2 Import", "SBOL2 Export"] +tags: ["Design", "Visualization", "Repository"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). @@ -34,8 +34,8 @@ SBOLDesigner 2.1 is a simple, biologist-friendly CAD software tool for creating | | | | ---| ---| -| Contact Person | Doug Densmore | -| Organization(s) | Boston University | +| Contact Person | Chris Myers | +| Organization(s) | University of Colorado, Boulder | | Programming Language | Java/HTML/JS/CSS | | OS/Platform | Web | | Availability | Open-Source | diff --git a/content/applications/sbolgenbank/index.md b/content/applications/sbolgenbank/index.md index b22b2afe0..ec03e8469 100644 --- a/content/applications/sbolgenbank/index.md +++ b/content/applications/sbolgenbank/index.md @@ -1,7 +1,7 @@ --- title: SBOL <-> Genbank Converter summary: Loss-less interconversion of SBOL v1.1 and GenBank -tags: ["SBOL1 Import", "SBOL1 Export"] +tags: ["Converter"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/sbolme/index.md b/content/applications/sbolme/index.md index 9aa321b1e..ac1dca8ab 100644 --- a/content/applications/sbolme/index.md +++ b/content/applications/sbolme/index.md @@ -1,7 +1,7 @@ --- title: SBOLme summary: An open-access repository of SBOL 2-compliant biochemical parts for a wide range of metabolic engineering applications. -tags: ["Knowledge Management", "SBOL2 Export"] +tags: ["Repository"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/sbolvalidator/index.md b/content/applications/sbolvalidator/index.md index ab40ef1d4..45e913e10 100644 --- a/content/applications/sbolvalidator/index.md +++ b/content/applications/sbolvalidator/index.md @@ -1,7 +1,7 @@ --- title: SBOL Validator/Converter summary: A simple, easy-to-use software tool that allows for conversion between SBOL/GenBank/FASTA files using the Synthetic Biology Open Language (SBOL) 2.0 data model. -tags: ["Knowledge Management", "SBOL1 Import", "SBOL1 Export", "SBOL2 Import", "SBOL2 Export"] +tags: ["Converter", "Repository"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/shortbol/index.md b/content/applications/shortbol/index.md index 8d6e99aac..c2532299c 100644 --- a/content/applications/shortbol/index.md +++ b/content/applications/shortbol/index.md @@ -1,8 +1,9 @@ --- title: ShortBOL summary: A shorthand language for SBOL -tags: ["Sequence Design","Circuit Design","SBOL2 Export"] +tags: ["Design"] date: "2020-06-30T00:00:00Z" +active: false # Optional external URL for project (replaces project detail page). external_link: "" diff --git a/content/applications/synbiohub/index.md b/content/applications/synbiohub/index.md index 5e1d7c4a8..804ba6a04 100644 --- a/content/applications/synbiohub/index.md +++ b/content/applications/synbiohub/index.md @@ -1,7 +1,7 @@ --- title: SynBioHub summary: A registry for storing and sharing genetic circuit designs using the SBOL2 standard -tags: ["Knowledge Management","Visualization", "SBOL Visual", "SBOL1 Import", "SBOL2 Import", "SBOL2 Export"] +tags: ["Repository", "Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/tellurium/index.md b/content/applications/tellurium/index.md index d2801e542..535ef9542 100644 --- a/content/applications/tellurium/index.md +++ b/content/applications/tellurium/index.md @@ -1,7 +1,7 @@ --- title: Tellurium summary: A Python environment based on spyder2 IDE, designed for systems and synthetic biology simulations. -tags: ["Sequence Design", "Circuit Design", "Modeling", "SBOL Visual", "SBOL1 Import", "SBOL1 Export"] +tags: ["Design", "Simulation"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/tinkercell/index.md b/content/applications/tinkercell/index.md index 472154906..56bbedfbb 100644 --- a/content/applications/tinkercell/index.md +++ b/content/applications/tinkercell/index.md @@ -1,8 +1,10 @@ --- title: TinkerCell summary: A widely used open source network design and simulation application tool for synthetic biology -tags: ["Circuit Design", "Modeling", "Visualization", "SBOL Visual", "SBOL1 Import", "SBOL1 Export"] +tags: ["Design", "Simulation", "Visualization"] date: "2020-06-30T00:00:00Z" +active: false + # Optional external URL for project (replaces project detail page). external_link: "" diff --git a/content/applications/visbol/index.md b/content/applications/visbol/index.md index 20db705eb..277628a4c 100644 --- a/content/applications/visbol/index.md +++ b/content/applications/visbol/index.md @@ -1,7 +1,7 @@ --- title: VisBOL summary: A JavaScript software library to visualize DNA features from SBOL2 documents using the SBOL Visual standard. -tags: ["Visualization", "SBOL Visual", "SBOL2 Import"] +tags: ["Visualization"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/applications/vpr/index.md b/content/applications/vpr/index.md index e0e865881..9b35a5505 100644 --- a/content/applications/vpr/index.md +++ b/content/applications/vpr/index.md @@ -1,7 +1,7 @@ --- title: Virtual Parts Repository summary: A repository of modular models of biological components. -tags: ["Knowledge Management", "Circuit Design", "Modeling", "SBOL Visual", "SBOL1 Import", "SBOL1 Export", "SBOL2 Export"] +tags: ["Design", "Simulation", "Repository"] date: "2020-06-30T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/authors/admin/_index.md b/content/authors/admin/_index.md index 36a29d441..b0748933e 100644 --- a/content/authors/admin/_index.md +++ b/content/authors/admin/_index.md @@ -80,6 +80,22 @@ user_groups: - Visitors --- + +
+ + SBOL for Biologists +
For Biologists
+ + + SBOL for Developers +
For Developers
+ + + Join SBOL +
Join the Community
+ +
+ Welcome to the Synthetic Biology Open Language (SBOL) community portal! diff --git a/content/authors/angel-goni-moreno/_index.md b/content/authors/angel-goni-moreno/_index.md new file mode 100644 index 000000000..5a6087dbc --- /dev/null +++ b/content/authors/angel-goni-moreno/_index.md @@ -0,0 +1,9 @@ +--- +title: Angel Goñi Moreno +role: Former SBOL Editor +organizations: + - name: Newcastle University + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/angel-goni-moreno/avatar.png b/content/authors/angel-goni-moreno/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/angel-goni-moreno/avatar.png differ diff --git a/content/authors/anil-wipat/_index.md b/content/authors/anil-wipat/_index.md new file mode 100644 index 000000000..292f4d1cb --- /dev/null +++ b/content/authors/anil-wipat/_index.md @@ -0,0 +1,10 @@ +--- +title: Anil Wipat +role: "SBOL Chair (2015–2019)" +weight: 30 +organizations: + - name: Newcastle University + url: "" +user_groups: + - Past Chairs +--- diff --git a/content/authors/anil-wipat/avatar.png b/content/authors/anil-wipat/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/anil-wipat/avatar.png differ diff --git a/content/authors/bryan-bartley/_index.md b/content/authors/bryan-bartley/_index.md new file mode 100644 index 000000000..2f6236e9a --- /dev/null +++ b/content/authors/bryan-bartley/_index.md @@ -0,0 +1,9 @@ +--- +title: Bryan Bartley +role: Former SBOL Editor +organizations: + - name: University of Washington + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/bryan-bartley/avatar.png b/content/authors/bryan-bartley/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/bryan-bartley/avatar.png differ diff --git a/content/authors/carolus-vitalis/_index.md b/content/authors/carolus-vitalis/_index.md new file mode 100644 index 000000000..229b99d71 --- /dev/null +++ b/content/authors/carolus-vitalis/_index.md @@ -0,0 +1,9 @@ +--- +title: Carolus Vitalis +role: SBOL Editor +organizations: + - name: University of Colorado + url: "" +user_groups: + - Current Editors +--- diff --git a/content/authors/carolus-vitalis/avatar.png b/content/authors/carolus-vitalis/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/carolus-vitalis/avatar.png differ diff --git a/content/authors/cesar-rodriguez/_index.md b/content/authors/cesar-rodriguez/_index.md new file mode 100644 index 000000000..351403d74 --- /dev/null +++ b/content/authors/cesar-rodriguez/_index.md @@ -0,0 +1,9 @@ +--- +title: Cesar Rodriguez +role: Former SBOL Editor +organizations: + - name: Autodesk + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/cesar-rodriguez/avatar.png b/content/authors/cesar-rodriguez/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/cesar-rodriguez/avatar.png differ diff --git a/content/authors/chris-myers/_index.md b/content/authors/chris-myers/_index.md new file mode 100644 index 000000000..7f61550a8 --- /dev/null +++ b/content/authors/chris-myers/_index.md @@ -0,0 +1,11 @@ +--- +title: Chris Myers +role: "SBOL Chair (2019–2023)" +weight: 20 +organizations: + - name: University of Colorado, Boulder + url: "" +user_groups: + - Past Chairs + - Steering Committee +--- diff --git a/content/authors/chris-myers/avatar.png b/content/authors/chris-myers/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/chris-myers/avatar.png differ diff --git a/content/authors/chris-voigt/_index.md b/content/authors/chris-voigt/_index.md new file mode 100644 index 000000000..a52b51718 --- /dev/null +++ b/content/authors/chris-voigt/_index.md @@ -0,0 +1,9 @@ +--- +title: Chris Voigt +role: Advisory Board +organizations: + - name: Massachusetts Institute of Technology + url: "" +user_groups: + - Past Advisory Board Members +--- diff --git a/content/authors/chris-voigt/avatar.png b/content/authors/chris-voigt/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/chris-voigt/avatar.png differ diff --git a/content/authors/claudia-vickers/_index.md b/content/authors/claudia-vickers/_index.md new file mode 100644 index 000000000..ecfc64822 --- /dev/null +++ b/content/authors/claudia-vickers/_index.md @@ -0,0 +1,9 @@ +--- +title: Claudia Vickers +role: Advisory Board +organizations: + - name: University of Queensland + url: "" +user_groups: + - Past Advisory Board Members +--- diff --git a/content/authors/claudia-vickers/avatar.png b/content/authors/claudia-vickers/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/claudia-vickers/avatar.png differ diff --git a/content/authors/curtis-madsen/_index.md b/content/authors/curtis-madsen/_index.md new file mode 100644 index 000000000..b8a3dbcaa --- /dev/null +++ b/content/authors/curtis-madsen/_index.md @@ -0,0 +1,9 @@ +--- +title: Curtis Madsen +role: Former SBOL Editor +organizations: + - name: Sandia National Labs + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/curtis-madsen/avatar.png b/content/authors/curtis-madsen/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/curtis-madsen/avatar.png differ diff --git a/content/authors/david-ross/_index.md b/content/authors/david-ross/_index.md new file mode 100644 index 000000000..5b776c3e4 --- /dev/null +++ b/content/authors/david-ross/_index.md @@ -0,0 +1,9 @@ +--- +title: David Ross +role: Steering Committee +organizations: + - name: NIST + url: "" +user_groups: + - Steering Committee +--- diff --git a/content/authors/david-ross/avatar.png b/content/authors/david-ross/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/david-ross/avatar.png differ diff --git a/content/authors/elizabeth-strychalski/_index.md b/content/authors/elizabeth-strychalski/_index.md new file mode 100644 index 000000000..e6f3e1b8e --- /dev/null +++ b/content/authors/elizabeth-strychalski/_index.md @@ -0,0 +1,9 @@ +--- +title: Elizabeth Strychalski +role: Advisory Board +organizations: + - name: National Institute of Standards and Technology + url: "" +user_groups: + - Past Advisory Board Members +--- diff --git a/content/authors/elizabeth-strychalski/avatar.png b/content/authors/elizabeth-strychalski/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/elizabeth-strychalski/avatar.png differ diff --git a/content/authors/erik-kubaczka/_index.md b/content/authors/erik-kubaczka/_index.md new file mode 100644 index 000000000..d572d7ecd --- /dev/null +++ b/content/authors/erik-kubaczka/_index.md @@ -0,0 +1,9 @@ +--- +title: Erik Kubaczka +role: SBOL Editor +organizations: + - name: Technical University of Darmstadt + url: "" +user_groups: + - Current Editors +--- diff --git a/content/authors/erik-kubaczka/avatar.png b/content/authors/erik-kubaczka/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/erik-kubaczka/avatar.png differ diff --git a/content/authors/ernst-oberortner/_index.md b/content/authors/ernst-oberortner/_index.md new file mode 100644 index 000000000..970f5988b --- /dev/null +++ b/content/authors/ernst-oberortner/_index.md @@ -0,0 +1,9 @@ +--- +title: Ernst Oberortner +role: Former SBOL Editor +organizations: + - name: Boston University + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/ernst-oberortner/avatar.png b/content/authors/ernst-oberortner/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/ernst-oberortner/avatar.png differ diff --git a/content/authors/felipe-buson/_index.md b/content/authors/felipe-buson/_index.md new file mode 100644 index 000000000..5eb59bde4 --- /dev/null +++ b/content/authors/felipe-buson/_index.md @@ -0,0 +1,9 @@ +--- +title: Felipe Buson +role: SBOL Editor +organizations: + - name: University of Bristol + url: "" +user_groups: + - Current Editors +--- diff --git a/content/authors/felipe-buson/avatar.png b/content/authors/felipe-buson/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/felipe-buson/avatar.png differ diff --git a/content/authors/georgie-hau-sorensen/_index.md b/content/authors/georgie-hau-sorensen/_index.md new file mode 100644 index 000000000..abf6b16c5 --- /dev/null +++ b/content/authors/georgie-hau-sorensen/_index.md @@ -0,0 +1,9 @@ +--- +title: Georgie Hau Sørensen +role: SBOL Editor +organizations: + - name: University of Bristol + url: "" +user_groups: + - Current Editors +--- diff --git a/content/authors/georgie-hau-sorensen/avatar.png b/content/authors/georgie-hau-sorensen/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/georgie-hau-sorensen/avatar.png differ diff --git a/content/authors/goksel-misirli/_index.md b/content/authors/goksel-misirli/_index.md new file mode 100644 index 000000000..4b0da733c --- /dev/null +++ b/content/authors/goksel-misirli/_index.md @@ -0,0 +1,10 @@ +--- +title: Goksel Misirli +role: Steering Committee +organizations: + - name: Keele University + url: "" +user_groups: + - Steering Committee + - Past Editors +--- diff --git a/content/authors/goksel-misirli/avatar.png b/content/authors/goksel-misirli/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/goksel-misirli/avatar.png differ diff --git a/content/authors/gonzalo-vidal-pena/_index.md b/content/authors/gonzalo-vidal-pena/_index.md new file mode 100644 index 000000000..92f05689f --- /dev/null +++ b/content/authors/gonzalo-vidal-pena/_index.md @@ -0,0 +1,10 @@ +--- +title: Gonzalo Vidal Peña +role: Former SBOL Editor +organizations: + - name: Newcastle University + url: "" +user_groups: + - Steering Committee + - Past Editors +--- diff --git a/content/authors/gonzalo-vidal-pena/avatar.png b/content/authors/gonzalo-vidal-pena/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/gonzalo-vidal-pena/avatar.png differ diff --git a/content/authors/hasan-baig/_index.md b/content/authors/hasan-baig/_index.md new file mode 100644 index 000000000..0cd1cc2bc --- /dev/null +++ b/content/authors/hasan-baig/_index.md @@ -0,0 +1,9 @@ +--- +title: Hasan Baig +role: Former SBOL Editor +organizations: + - name: University of Connecticut + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/hasan-baig/avatar.png b/content/authors/hasan-baig/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/hasan-baig/avatar.png differ diff --git a/content/authors/hennig-hermjakob/_index.md b/content/authors/hennig-hermjakob/_index.md new file mode 100644 index 000000000..c171e72e5 --- /dev/null +++ b/content/authors/hennig-hermjakob/_index.md @@ -0,0 +1,9 @@ +--- +title: Hennig Hermjakob +role: Advisory Board +organizations: + - name: EMBL-EBI + url: "" +user_groups: + - Past Advisory Board Members +--- diff --git a/content/authors/hennig-hermjakob/avatar.png b/content/authors/hennig-hermjakob/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/hennig-hermjakob/avatar.png differ diff --git a/content/authors/herbert-sauro/_index.md b/content/authors/herbert-sauro/_index.md new file mode 100644 index 000000000..eb81da73f --- /dev/null +++ b/content/authors/herbert-sauro/_index.md @@ -0,0 +1,10 @@ +--- +title: Herbert Sauro +role: "SBOL Chair (2010–2015)" +weight: 40 +organizations: + - name: University of Washington + url: "" +user_groups: + - Past Chairs +--- diff --git a/content/authors/herbert-sauro/avatar.png b/content/authors/herbert-sauro/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/herbert-sauro/avatar.png differ diff --git a/content/authors/jacob-beal/_index.md b/content/authors/jacob-beal/_index.md new file mode 100644 index 000000000..dfb4d598b --- /dev/null +++ b/content/authors/jacob-beal/_index.md @@ -0,0 +1,10 @@ +--- +title: Jacob Beal +role: Steering Committee +organizations: + - name: Raytheon BBN Technologies + url: "" +user_groups: + - Steering Committee + - Past Editors +--- diff --git a/content/authors/jacob-beal/avatar.png b/content/authors/jacob-beal/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/jacob-beal/avatar.png differ diff --git a/content/authors/jacqueline-quinn/_index.md b/content/authors/jacqueline-quinn/_index.md new file mode 100644 index 000000000..a6c039b67 --- /dev/null +++ b/content/authors/jacqueline-quinn/_index.md @@ -0,0 +1,9 @@ +--- +title: Jacqueline Quinn +role: Former SBOL Editor +organizations: + - name: Google + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/jacqueline-quinn/avatar.png b/content/authors/jacqueline-quinn/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/jacqueline-quinn/avatar.png differ diff --git a/content/authors/james-mclaughlin/_index.md b/content/authors/james-mclaughlin/_index.md new file mode 100644 index 000000000..9cc3d86cc --- /dev/null +++ b/content/authors/james-mclaughlin/_index.md @@ -0,0 +1,9 @@ +--- +title: James McLaughlin +role: Former SBOL Editor +organizations: + - name: Newcastle University + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/james-mclaughlin/avatar.png b/content/authors/james-mclaughlin/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/james-mclaughlin/avatar.png differ diff --git a/content/authors/james-scott-brown/_index.md b/content/authors/james-scott-brown/_index.md new file mode 100644 index 000000000..a54c4e70b --- /dev/null +++ b/content/authors/james-scott-brown/_index.md @@ -0,0 +1,9 @@ +--- +title: James Scott-Brown +role: Former SBOL Editor +organizations: + - name: University of Oxford + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/james-scott-brown/avatar.png b/content/authors/james-scott-brown/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/james-scott-brown/avatar.png differ diff --git a/content/authors/jean-peccoud/_index.md b/content/authors/jean-peccoud/_index.md new file mode 100644 index 000000000..062582443 --- /dev/null +++ b/content/authors/jean-peccoud/_index.md @@ -0,0 +1,9 @@ +--- +title: Jean Peccoud +role: Advisory Board +organizations: + - name: Colorado State University + url: "" +user_groups: + - Past Advisory Board Members +--- diff --git a/content/authors/jean-peccoud/avatar.png b/content/authors/jean-peccoud/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/jean-peccoud/avatar.png differ diff --git a/content/authors/kevin-clancy/_index.md b/content/authors/kevin-clancy/_index.md new file mode 100644 index 000000000..2baa02dbe --- /dev/null +++ b/content/authors/kevin-clancy/_index.md @@ -0,0 +1,9 @@ +--- +title: Kevin Clancy +role: Former SBOL Editor +organizations: + - name: ThermoFisher + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/kevin-clancy/avatar.png b/content/authors/kevin-clancy/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/kevin-clancy/avatar.png differ diff --git a/content/authors/lukas-buecherl/_index.md b/content/authors/lukas-buecherl/_index.md new file mode 100644 index 000000000..f8f52377d --- /dev/null +++ b/content/authors/lukas-buecherl/_index.md @@ -0,0 +1,10 @@ +--- +title: Lukas Buecherl +role: Former SBOL Editor +organizations: + - name: Utah State University + url: "" +user_groups: + - Steering Committee + - Past Editors +--- diff --git a/content/authors/lukas-buecherl/avatar.png b/content/authors/lukas-buecherl/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/lukas-buecherl/avatar.png differ diff --git a/content/authors/mandy-wilson/_index.md b/content/authors/mandy-wilson/_index.md new file mode 100644 index 000000000..86b6d7294 --- /dev/null +++ b/content/authors/mandy-wilson/_index.md @@ -0,0 +1,9 @@ +--- +title: Mandy Wilson +role: Former SBOL Editor +organizations: + - name: Virginia Bioinformatics Institute + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/mandy-wilson/avatar.png b/content/authors/mandy-wilson/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/mandy-wilson/avatar.png differ diff --git a/content/authors/manuel-porcar-miralles/_index.md b/content/authors/manuel-porcar-miralles/_index.md new file mode 100644 index 000000000..53d6d21ea --- /dev/null +++ b/content/authors/manuel-porcar-miralles/_index.md @@ -0,0 +1,9 @@ +--- +title: Manuel Porcar Miralles +role: Advisory Board +organizations: + - name: I2SysBio + url: "" +user_groups: + - Past Advisory Board Members +--- diff --git a/content/authors/manuel-porcar-miralles/avatar.png b/content/authors/manuel-porcar-miralles/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/manuel-porcar-miralles/avatar.png differ diff --git a/content/authors/matthew-pocock/_index.md b/content/authors/matthew-pocock/_index.md new file mode 100644 index 000000000..9088e0d4d --- /dev/null +++ b/content/authors/matthew-pocock/_index.md @@ -0,0 +1,9 @@ +--- +title: Matthew Pocock +role: Former SBOL Editor +organizations: + - name: Newcastle University + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/matthew-pocock/avatar.png b/content/authors/matthew-pocock/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/matthew-pocock/avatar.png differ diff --git a/content/authors/metehan-unal/_index.md b/content/authors/metehan-unal/_index.md new file mode 100644 index 000000000..9d387f689 --- /dev/null +++ b/content/authors/metehan-unal/_index.md @@ -0,0 +1,9 @@ +--- +title: Metehan Unal +role: SBOL Editor +organizations: + - name: Keele University + url: "" +user_groups: + - Current Editors +--- diff --git a/content/authors/metehan-unal/avatar.png b/content/authors/metehan-unal/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/metehan-unal/avatar.png differ diff --git a/content/authors/michal-galdzicki/_index.md b/content/authors/michal-galdzicki/_index.md new file mode 100644 index 000000000..707c66d2a --- /dev/null +++ b/content/authors/michal-galdzicki/_index.md @@ -0,0 +1,9 @@ +--- +title: Michal Galdzicki +role: Former SBOL Editor +organizations: + - name: University of Washington + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/michal-galdzicki/avatar.png b/content/authors/michal-galdzicki/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/michal-galdzicki/avatar.png differ diff --git a/content/authors/nicholas-roehner/_index.md b/content/authors/nicholas-roehner/_index.md new file mode 100644 index 000000000..f58576192 --- /dev/null +++ b/content/authors/nicholas-roehner/_index.md @@ -0,0 +1,9 @@ +--- +title: Nicholas Roehner +role: Former SBOL Editor +organizations: + - name: BBN Technologies + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/nicholas-roehner/avatar.png b/content/authors/nicholas-roehner/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/nicholas-roehner/avatar.png differ diff --git a/content/authors/pedro-fontanarrosa/_index.md b/content/authors/pedro-fontanarrosa/_index.md new file mode 100644 index 000000000..00508378a --- /dev/null +++ b/content/authors/pedro-fontanarrosa/_index.md @@ -0,0 +1,9 @@ +--- +title: Pedro Fontanarrosa +role: Former SBOL Editor +organizations: + - name: University of Utah + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/pedro-fontanarrosa/avatar.png b/content/authors/pedro-fontanarrosa/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/pedro-fontanarrosa/avatar.png differ diff --git a/content/authors/prashant-vaidyanathan/_index.md b/content/authors/prashant-vaidyanathan/_index.md new file mode 100644 index 000000000..92eb9e6ff --- /dev/null +++ b/content/authors/prashant-vaidyanathan/_index.md @@ -0,0 +1,11 @@ +--- +title: Prashant Vaidyanathan +role: "SBOL Chair (2023–present)" +weight: 10 +organizations: + - name: Oxford Biomedica + url: "" +user_groups: + - Current Chair + - Past Editors +--- diff --git a/content/authors/prashant-vaidyanathan/avatar.png b/content/authors/prashant-vaidyanathan/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/prashant-vaidyanathan/avatar.png differ diff --git a/content/authors/raik-grunberg/_index.md b/content/authors/raik-grunberg/_index.md new file mode 100644 index 000000000..195e89b2e --- /dev/null +++ b/content/authors/raik-grunberg/_index.md @@ -0,0 +1,9 @@ +--- +title: Raik Grünberg +role: Former SBOL Editor +organizations: + - name: University of Montreal + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/raik-grunberg/avatar.png b/content/authors/raik-grunberg/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/raik-grunberg/avatar.png differ diff --git a/content/authors/robert-sidney-cox/_index.md b/content/authors/robert-sidney-cox/_index.md new file mode 100644 index 000000000..52b645e8e --- /dev/null +++ b/content/authors/robert-sidney-cox/_index.md @@ -0,0 +1,9 @@ +--- +title: Robert Sidney Cox +role: Former SBOL Editor +organizations: + - name: Kobe University + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/robert-sidney-cox/avatar.png b/content/authors/robert-sidney-cox/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/robert-sidney-cox/avatar.png differ diff --git a/content/authors/thomas-gorochowski/_index.md b/content/authors/thomas-gorochowski/_index.md new file mode 100644 index 000000000..8fbb042d4 --- /dev/null +++ b/content/authors/thomas-gorochowski/_index.md @@ -0,0 +1,9 @@ +--- +title: Thomas Gorochowski +role: Steering Committee +organizations: + - name: University of Bristol + url: "" +user_groups: + - Steering Committee +--- diff --git a/content/authors/thomas-gorochowski/avatar.png b/content/authors/thomas-gorochowski/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/thomas-gorochowski/avatar.png differ diff --git a/content/authors/tom-mitchell/_index.md b/content/authors/tom-mitchell/_index.md new file mode 100644 index 000000000..c09b080de --- /dev/null +++ b/content/authors/tom-mitchell/_index.md @@ -0,0 +1,9 @@ +--- +title: Tom Mitchell +role: Former SBOL Editor +organizations: + - name: Raytheon BBN Technologies + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/tom-mitchell/avatar.png b/content/authors/tom-mitchell/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/tom-mitchell/avatar.png differ diff --git a/content/authors/traci-haddock/_index.md b/content/authors/traci-haddock/_index.md new file mode 100644 index 000000000..0a7200451 --- /dev/null +++ b/content/authors/traci-haddock/_index.md @@ -0,0 +1,9 @@ +--- +title: Traci Haddock +role: Advisory Board +organizations: + - name: iGEM Foundation + url: "" +user_groups: + - Past Advisory Board Members +--- diff --git a/content/authors/traci-haddock/avatar.png b/content/authors/traci-haddock/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/traci-haddock/avatar.png differ diff --git a/content/authors/tramy-nguyen/_index.md b/content/authors/tramy-nguyen/_index.md new file mode 100644 index 000000000..e93c76cf7 --- /dev/null +++ b/content/authors/tramy-nguyen/_index.md @@ -0,0 +1,9 @@ +--- +title: Tramy Nguyen +role: Former SBOL Editor +organizations: + - name: University of Utah + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/tramy-nguyen/avatar.png b/content/authors/tramy-nguyen/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/tramy-nguyen/avatar.png differ diff --git a/content/authors/umesh-p/_index.md b/content/authors/umesh-p/_index.md new file mode 100644 index 000000000..8a39d4df8 --- /dev/null +++ b/content/authors/umesh-p/_index.md @@ -0,0 +1,9 @@ +--- +title: Umesh P +role: Former SBOL Editor +organizations: + - name: Kerala Technological University + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/umesh-p/avatar.png b/content/authors/umesh-p/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/umesh-p/avatar.png differ diff --git a/content/authors/vishwesh-kulkarni/_index.md b/content/authors/vishwesh-kulkarni/_index.md new file mode 100644 index 000000000..0fc561b8c --- /dev/null +++ b/content/authors/vishwesh-kulkarni/_index.md @@ -0,0 +1,9 @@ +--- +title: Vishwesh Kulkarni +role: Former SBOL Editor +organizations: + - name: University of Warwick + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/vishwesh-kulkarni/avatar.png b/content/authors/vishwesh-kulkarni/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/vishwesh-kulkarni/avatar.png differ diff --git a/content/authors/yan-kay-ho/_index.md b/content/authors/yan-kay-ho/_index.md new file mode 100644 index 000000000..fe3b9932b --- /dev/null +++ b/content/authors/yan-kay-ho/_index.md @@ -0,0 +1,9 @@ +--- +title: Yan-Kay Ho +role: Steering Committee +organizations: + - name: University of Cambridge + url: "" +user_groups: + - Steering Committee +--- diff --git a/content/authors/yan-kay-ho/avatar.png b/content/authors/yan-kay-ho/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/yan-kay-ho/avatar.png differ diff --git a/content/authors/zach-palchik/_index.md b/content/authors/zach-palchik/_index.md new file mode 100644 index 000000000..b0f874b19 --- /dev/null +++ b/content/authors/zach-palchik/_index.md @@ -0,0 +1,9 @@ +--- +title: Zach Palchik +role: Former SBOL Editor +organizations: + - name: Zymergen + url: "" +user_groups: + - Past Editors +--- diff --git a/content/authors/zach-palchik/avatar.png b/content/authors/zach-palchik/avatar.png new file mode 100644 index 000000000..21532ff24 Binary files /dev/null and b/content/authors/zach-palchik/avatar.png differ diff --git a/content/biologist/_index.md b/content/biologist/_index.md new file mode 100644 index 000000000..ff27c2686 --- /dev/null +++ b/content/biologist/_index.md @@ -0,0 +1,49 @@ +--- +title: "SBOL for Biologists" +subtitle: "No coding required. Give your designs a shared language that tools, collaborators, and journals all understand." + +benefits: + - icon: "fas fa-share-alt" + title: "Share Reproducibly" + description: "SBOL captures the full intent of your design - parts, interactions, and context - so collaborators always get exactly what you meant." + - icon: "fas fa-file-alt" + title: "Publish with Confidence" + description: "Deposit your designs in repositories like SynBioHub and cite them directly in papers with persistent, stable links." + - icon: "fas fa-drafting-compass" + title: "Speak a Visual Language" + description: "SBOL Visual provides standardised glyphs so your diagrams are immediately understood by any synthetic biologist, worldwide." + +tools: + - name: "SBOLCanvas" + description: "A web-based tool for creating publication-ready, standards-compliant genetic diagrams - no installation needed." + bullets: + - "Drag-and-drop interface for building complex designs intuitively" + - "Uses standardised SBOL Visual glyphs for every part type" + - "Export high-quality images ready for manuscripts and presentations" + image: "sbolcanvas.png" + image_alt: "SBOLCanvas Interface" + url: "https://sbolcanvas.org" + cta_text: "Open SBOLCanvas" + flip: false + - name: "SynBioHub" + description: "The shared repository for synthetic biology - think of it as GitHub for genetic designs." + bullets: + - "Store your parts and designs securely in one place" + - "Share with collaborators or publish openly with a persistent, citable link" + - "Search thousands of existing parts to reuse in your own experiments" + image: "synbiohub.png" + image_alt: "SynBioHub Interface" + url: "https://synbiohub.org" + cta_text: "Visit SynBioHub" + flip: true + +glyphs_title: "The Visual Language of Synthetic Biology" +glyphs_description: "SBOL Visual defines a standardised set of glyphs - symbols for promoters, CDSs, terminators, and more - so diagrams mean the same thing everywhere. Whether you are annotating a figure for a paper or describing a construct to a collaborator, SBOL Visual gives you a shared vocabulary the whole community recognises." +glyphs_url: "/visual-glyphs" +glyphs_history_url: "/sbolv-10-years" +glyphs_gallery_url: "/visual-gallery" + +genai_title: "Learn SBOL with AI" +genai_description: "Not sure where to start? Our SBOL GPT assistants can answer questions about the standard in plain language - no documentation required." +genai_url: "/genai-tools" +--- diff --git a/content/biologist/sbolcanvas.png b/content/biologist/sbolcanvas.png new file mode 100644 index 000000000..36dc7ff3b Binary files /dev/null and b/content/biologist/sbolcanvas.png differ diff --git a/content/biologist/synbiohub.png b/content/biologist/synbiohub.png new file mode 100644 index 000000000..6994b32bb Binary files /dev/null and b/content/biologist/synbiohub.png differ diff --git a/content/blog/_index.md b/content/blog/_index.md new file mode 100644 index 000000000..3e179853a --- /dev/null +++ b/content/blog/_index.md @@ -0,0 +1,4 @@ +--- +title: Blog +view: 3 +--- diff --git a/content/blog/welcome-to-sbol-blog/index.md b/content/blog/welcome-to-sbol-blog/index.md new file mode 100644 index 000000000..1dded555b --- /dev/null +++ b/content/blog/welcome-to-sbol-blog/index.md @@ -0,0 +1,17 @@ +--- +title: "Welcome to the SBOL Blog" +date: 2026-05-17 +authors: ["prashant-vaidyanathan"] +tags: ["synthetic biology", "SBOL", "community"] +summary: "Introducing the new SBOL community blog — a space for developers, researchers, and users to share insights, tutorials, and updates from across the synthetic biology community." +featured: false +image: + caption: "" + focal_point: "" +--- + +Welcome to the SBOL community blog. This is a space for developers, researchers, and users of the Synthetic Biology Open Language to share insights, tutorials, tools, and perspectives. + +Whether you are building a new library, publishing a design workflow, or exploring SBOL for the first time, this blog is a venue to connect with the broader community and learn from one another. + +Stay tuned for upcoming posts from contributors across the community. diff --git a/content/community-governance/_index.md b/content/community-governance/_index.md index cb9d6378b..51ef47a74 100644 --- a/content/community-governance/_index.md +++ b/content/community-governance/_index.md @@ -72,41 +72,7 @@ The SBOL Editors shall hold weekly meetings to coordinate their execution of the The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. -SBOL Editors are elected by a community vote, following the process below. Editors serve initially for a two-year term, and upon unanimous approval of the editors and chair, an editor's term can be extended for an additional third year. After completing their term as editor, a person may not run for editor again for at least one year. To maximize continuity, editors' terms should be de-synchronized. There are 5 editorial positions, currently held by: - -* Lukas Buecherl, Utah State University -* Felipe Buson, University of Bristol -* Erik Kubaczka, Technical University of Darmstadt -* Georgie Hau Sørensen, University of Bristol -* Carolus Vitalis, University of Colorado - -Previous SBOL Editors (including their affiliation when they were editors): -* Tom Mitchell (Raytheon BBN Technologies) -* Gonzalo Vidal Peña (Newcastle University) -* James Scott-Brown (University of Oxford) -* Prashant Vaidyananthan (Microsoft Research) -* Pedro Fontanarrosa (University of Utah) -* Hasan Baig (University of Connecticut) -* Vishwesh Kulkarni (University of Warwick) -* Zach Palchik (Zymergen) -* Curtis Madsen (Sandia National Labs) -* Nicholas Roehner (BBN Technologies) -* Angel Goñi Moreno (Newcastle University) -* Umesh P (Kerala Technological University) -* Tramy Nguyen (University of Utah) -* James McLaughlin (Newcastle University) -* Robert Sidney Cox (Kobe University) -* Raik Grunberg (University of Montreal) -* Jacob Beal (BBN Technologies) -* Bryan Bartley (University of Washington) -* Kevin Clancy (ThermoFisher) -* Michal Galdzicki (University of Washington) -* Goksel Misirli (Newcastle University) -* Ernst Oberortner (Boston University) -* Matthew Pocock, (Newcastle University) -* Jacqueline Quinn (Google) -* Cesar Rodriguez (Autodesk) -* Mandy Wilson (Virginia Bioinformatics Institute). +SBOL Editors are elected by a community vote, following the process below. Editors serve initially for a two-year term, and upon unanimous approval of the editors and chair, an editor's term can be extended for an additional third year. After completing their term as editor, a person may not run for editor again for at least one year. To maximize continuity, editors' terms should be de-synchronized. There are 5 editorial positions. For the current list of editors, see the [Community Leadership](/community-leadership/) page. ## SBOL Chair and Steering Committee The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. @@ -121,48 +87,7 @@ The SBOL Steering Committee shall hold monthly meetings to coordinate around str The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. -The SBOL current chair: - -**Prashant Vaidyanathan (April, 2023-), Oxford Biomedica** - -Previous Chairs: - -* Chris Myers (2019-2023), University of Colorado, Boulder -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Colorado, Boulder - -Past SBOL Steering Committee Members (listed alphabetically): -* Kevin Clancy, Synthetic Genomics, Inc. -* Ernst Oberortner, Takara Bio, USA -* Timothy Rudge, Newcastle University, UK -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University, UK - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Board is currently (listed alphabetically): - -* Dr. Traci Haddock, iGEM Foundation -* Dr. Hennig Hermajakob, EMBL-EBI -* Prof. Jean Peccoud, Colorado State University -* Prof. Manuel Porcar Miralles, I2SysBio -* Dr. Elizabeth Strychalski, National Institute of Standards and Technology -* Prof. Claudia Vickers, University of Queensland -* Prof. Chris Voigt, Massachusetts Institute of Technology - - -Past SBOL Advisory Board Members (listed alphabetically): -* Prof. Matthew Chang, National University of Singapore -* Prof. Richard Kitney, Imperial College London -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University +For the current Chair, Steering Committee, and Advisory Board, see the [Community Leadership](/community-leadership/) page. ## SBOL Industrial Consortium The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. @@ -192,7 +117,7 @@ Candidates are elected by plurality. 5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. +6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate "rough consensus". 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. 2. The reasons for decisions must be recorded with the results of the vote. 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. @@ -201,20 +126,20 @@ Candidates are elected by plurality. #### Voting form must: 1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” +2. State the eligibility criteria for voting, "All members of the SBOL Developers Group are eligible to vote." 3. Provide the following options for the vote: * accept — vote to accept the SEP * reject — vote to reject the SEP * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). + * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to "abstain" this vote will be counted when determining majorities). #### Ground-rules for moderating discussions in SBOL breakout sessions 1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. 2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. +3. Pause periodically for "step back" and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. 4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” + * e.g., "You are wrong" is problematic for communication because it is about people ("you") and value judgements ("wrong"). It will tend to promote rather than resolve conflict. + * Instead: "I am concerned that proposal X will have negative consequence Y." 5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. 6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/content/community-leadership/10-chair.md b/content/community-leadership/10-chair.md new file mode 100644 index 000000000..cf4abe563 --- /dev/null +++ b/content/community-leadership/10-chair.md @@ -0,0 +1,15 @@ ++++ +widget = "people" +headless = true +weight = 10 +title = "" + +[content] + user_groups = ["Current Chair"] + +[design] + show_social = true + show_interests = false + show_role = true + show_organizations = true ++++ diff --git a/content/community-leadership/20-editors.md b/content/community-leadership/20-editors.md new file mode 100644 index 000000000..08f2e08cf --- /dev/null +++ b/content/community-leadership/20-editors.md @@ -0,0 +1,15 @@ ++++ +widget = "people" +headless = true +weight = 20 +title = "" + +[content] + user_groups = ["Current Editors"] + +[design] + show_social = true + show_interests = false + show_role = false + show_organizations = true ++++ diff --git a/content/community-leadership/30-steering.md b/content/community-leadership/30-steering.md new file mode 100644 index 000000000..7023b83ac --- /dev/null +++ b/content/community-leadership/30-steering.md @@ -0,0 +1,15 @@ ++++ +widget = "people" +headless = true +weight = 30 +title = "" + +[content] + user_groups = ["Steering Committee"] + +[design] + show_social = true + show_interests = false + show_role = false + show_organizations = true ++++ diff --git a/content/community-leadership/40-past-advisory.md b/content/community-leadership/40-past-advisory.md new file mode 100644 index 000000000..436b777b6 --- /dev/null +++ b/content/community-leadership/40-past-advisory.md @@ -0,0 +1,15 @@ ++++ +widget = "people" +headless = true +weight = 40 +title = "" + +[content] + user_groups = ["Past Advisory Board Members"] + +[design] + show_social = true + show_interests = false + show_role = false + show_organizations = true ++++ diff --git a/content/community-leadership/50-past-chairs.md b/content/community-leadership/50-past-chairs.md new file mode 100644 index 000000000..4a7a16100 --- /dev/null +++ b/content/community-leadership/50-past-chairs.md @@ -0,0 +1,15 @@ ++++ +widget = "people" +headless = true +weight = 50 +title = "" + +[content] + user_groups = ["Past Chairs"] + +[design] + show_social = false + show_interests = false + show_role = true + show_organizations = true ++++ diff --git a/content/community-leadership/60-past-editors.md b/content/community-leadership/60-past-editors.md new file mode 100644 index 000000000..2b3a873bf --- /dev/null +++ b/content/community-leadership/60-past-editors.md @@ -0,0 +1,15 @@ ++++ +widget = "people" +headless = true +weight = 60 +title = "" + +[content] + user_groups = ["Past Editors"] + +[design] + show_social = false + show_interests = false + show_role = false + show_organizations = true ++++ diff --git a/content/community-leadership/index.md b/content/community-leadership/index.md new file mode 100644 index 000000000..0de0b351b --- /dev/null +++ b/content/community-leadership/index.md @@ -0,0 +1,4 @@ ++++ +title = "Community Leadership" +type = "widget_page" ++++ diff --git a/content/community-meetings/_index.md b/content/community-meetings/_index.md index e1d627662..c310bee3e 100644 --- a/content/community-meetings/_index.md +++ b/content/community-meetings/_index.md @@ -1,56 +1,415 @@ --- -title: Meetings +title: Meetings & Outreach +subtitle: "The SBOL community meets approximately every six months at COMBINE and HARMONY workshops, and actively engages the broader synthetic biology community at conferences worldwide." +hero_btn_text: "Join us on Slack" +hero_btn_icon: "fab fa-slack" +hero_btn_url: "https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg" -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 +connect_text: "SBOL is open-source and thrives on active participation. Contribute code, join working groups, or simply stay informed." +connect_links: + - name: "GitHub" + description: "All things SBOL" + url: "https://github.com/SynBioDex" + - name: "Mailing List" + description: "Stay informed" + url: "https://groups.google.com/g/sbol-announce" + - name: "Join SBOL" + description: "Contact our editors" + url: "https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit" + - name: "YouTube" + description: "View SBOL videos" + url: "https://youtube.com/@syntheticbiologyopenlangua6204?si=j5PkGrh_-DSmbl2G" + -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL Developers community meets approximately every 6 months. The discussion at these workshops is often convivial, collegiate, and interesting. In May 2014 the SBOL Developers group elected to co-locate future SBOL workshops with similar workshops hosted by the ["Computational Modeling in Biolog Network (COMBINE)"](http://co.mbine.org/). This creates an atmosphere where synthetic biologists and systems biologists can work toward a common goal of integrating biological knowledge through inter-operable and non-overlapping data standards. Our “COMBINE”d efforts empower exciting innovations like [modeling whole cells](https://sites.google.com/site/vwwholecellsummerschool/). - -We welcome participants from industry to these discussions, as the SBOL standard exists to support commercial as well as scientific innovation in synthetic biology and biotechnology. +meetings: + - name: "COMBINE 2026" + type: "COMBINE" + date: "2026-09-07" + date_display: "Sep 2026" + location: "Keele University, UK" + url: "https://co.mbine.org/author/combine-2026/" + - name: "COMBINE 2024" + type: "COMBINE" + date: "2024-09-01" + date_display: "Sep 2024" + location: "Stuttgart, Germany" + url: "https://co.mbine.org/author/combine-2024/" + - name: "HARMONY 2024" + type: "HARMONY" + date: "2024-04-08" + date_display: "Apr 2024" + location: "University College London, UK" + url: "https://co.mbine.org/author/harmony-2024/" + - name: "COMBINE 2023" + type: "COMBINE" + date: "2023-10-05" + date_display: "Oct 2023" + location: "Farmington, CT, USA" + url: "https://co.mbine.org/author/combine-2023/" + - name: "HARMONY 2023" + type: "HARMONY" + date: "2023-04-24" + date_display: "Apr 2023" + location: "University of Washington, Seattle, WA, USA" + url: "https://co.mbine.org/author/harmony-2023/" + - name: "COMBINE 2022" + type: "COMBINE" + date: "2022-10-06" + date_display: "Oct 2022" + location: "Berlin, Germany" + url: "https://co.mbine.org/author/combine-2022/" + - name: "HARMONY 2022" + type: "HARMONY" + date: "2022-04-26" + date_display: "Apr 2022" + location: "Washington, DC (Hybrid)" + url: "/event/2022/harmony" + - name: "COMBINE 2021" + type: "COMBINE" + date: "2021-10-11" + date_display: "Oct 2021" + location: "Online (virtual)" + url: "/event/2021/combine" + - name: "HARMONY 2021" + type: "HARMONY" + date: "2021-03-22" + date_display: "Mar 2021" + location: "Online (virtual)" + url: "/event/2021/harmony" + - name: "COMBINE 2020" + type: "COMBINE" + date: "2020-10-05" + date_display: "Oct 2020" + location: "UConn Health, Connecticut, USA" + url: "http://old_co.mbine.org/events/COMBINE_2020" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2020/COMBINE20" + - name: "HARMONY 2020" + type: "HARMONY" + date: "2020-03-09" + date_display: "Mar 2020" + location: "EMBL-EBI, Cambridgeshire, UK" + url: "http://old_co.mbine.org/events/HARMONY_2020" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2020/HARMONY20" + - name: "COMBINE 2019" + type: "COMBINE" + date: "2019-07-15" + date_display: "Jul 2019" + location: "Studio Villa Bosch, Heidelberg, Germany" + url: "http://old_co.mbine.org/events/COMBINE_2019" + slides_url: "http://old_co.mbine.org/events/COMBINE_2019" + - name: "HARMONY 2019" + type: "HARMONY" + date: "2019-03-25" + date_display: "Mar 2019" + location: "Caltech, Pasadena, CA, USA" + url: "http://old_co.mbine.org/events/HARMONY_2019" + - name: "COMBINE 2018" + type: "COMBINE" + date: "2018-10-08" + date_display: "Oct 2018" + location: "Boston University, MA, USA" + url: "http://old_co.mbine.org/events/COMBINE_2018" + - name: "HARMONY 2018" + type: "HARMONY" + date: "2018-06-18" + date_display: "Jun 2018" + location: "Oxford University, UK" + url: "http://old_co.mbine.org/events/HARMONY_2018" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2018/HARMONY" + - name: "COMBINE 2017" + type: "COMBINE" + date: "2017-10-09" + date_display: "Oct 2017" + location: "Università degli Studi di Milano Bicocca, Italy" + url: "http://old_co.mbine.org/events/COMBINE_2017" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2017/COMBINE%202017" + - name: "HARMONY 2017" + type: "HARMONY" + date: "2017-06-26" + date_display: "Jun 2017" + location: "University of Washington, Seattle, WA, USA" + url: "http://old_co.mbine.org/events/HARMONY_2017" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2017/HARMONY" + - name: "COMBINE 2016" + type: "COMBINE" + date: "2016-09-19" + date_display: "Sep 2016" + location: "Newcastle University, Newcastle, UK" + url: "http://old_co.mbine.org/events/COMBINE_2016" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2016/COMBINE" + - name: "SBOL 14" + type: "SBOL Workshop" + date: "2016-03-14" + date_display: "Mar 2016" + location: "Raytheon BBN Technologies, Boston, MA, USA" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2016/15TH_SBOL" + - name: "COMBINE 2015" + type: "COMBINE" + date: "2015-10-12" + date_display: "Oct 2015" + location: "University of Utah, Salt Lake City, UT, USA" + url: "http://old_co.mbine.org/events/COMBINE_2015" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2015/COMBINE" + - name: "HARMONY 2015" + type: "HARMONY" + date: "2015-03-20" + date_display: "Mar 2015" + location: "Wittenberg, Germany" + - name: "COMBINE 2014" + type: "COMBINE" + date: "2014-08-18" + date_display: "Aug 2014" + location: "University of Southern California, Los Angeles, CA, USA" + url: "http://old_co.mbine.org/events/COMBINE_2014" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2014/COMBINE" + - name: "SBOL 10" + type: "SBOL Workshop" + date: "2014-01-07" + date_display: "Jan 2014" + location: "UC Berkeley, CA, USA" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2014/SBOL10" + - name: "SBOL 9" + type: "SBOL Workshop" + date: "2013-04-24" + date_display: "Apr 2013" + location: "Newcastle University, Newcastle, UK" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2013/SBOL9" + - name: "SBOL 8" + type: "SBOL Workshop" + date: "2012-11-07" + date_display: "Nov 2012" + location: "Boston University, MA, USA" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2012/SBOL8" + - name: "SBOL 7" + type: "SBOL Workshop" + date: "2012-06-05" + date_display: "Jun 2012" + location: "San Francisco, CA, USA" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2012/SBOL7" + - name: "SBOL 6" + type: "SBOL Workshop" + date: "2012-01-05" + date_display: "Jan 2012" + location: "University of Washington, Seattle, WA, USA" + slides_url: "https://github.com/SynBioDex/Community-Media/tree/master/2012/SBOL6" + - name: "SBOL 5" + type: "SBOL Workshop" + date: "2011-06-08" + date_display: "Jun 2011" + location: "San Diego, CA, USA" + - name: "SBOL 4" + type: "SBOL Workshop" + date: "2011-01-07" + date_display: "Jan 2011" + location: "Blacksburg, VA, USA" + - name: "SBOL 3" + type: "SBOL Workshop" + date: "2010-06-13" + date_display: "Jun 2010" + location: "Anaheim, CA, USA" + - name: "SBOL 2" + type: "SBOL Workshop" + date: "2009-07-26" + date_display: "Jul 2009" + location: "Stanford University, CA, USA" + slides_url: "https://github.com/SynBioDex/Community-Media/blob/master/2009/2nd_SBOL/Galdzicki_PoBoL_Update_26072009.pptx" + - name: "SBOL 1" + type: "SBOL Workshop" + date: "2008-04-27" + date_display: "Apr 2008" + location: "University of Washington, WA, USA" + slides_url: "https://github.com/SynBioDex/Community-Media/blob/master/2008/1ST_SBOL/workshop_book_042208.pdf" - -### SBOL Workshops and Conferences - -| Event | Date (YYYY-MM-DD) | Location | Materials | -|---------------------------------------------------------------------------------------|-------------------|------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------| -| [COMBINE 2024](https://co.mbine.org/author/combine-2024/) | 2024-09-01/05 | Stuttgart, Germany | | -| [HARMONY 2024](https://co.mbine.org/author/harmony-2024/) | 2024-04-08/11 | University College London, London, UK | | -| [COMBINE 2023](https://co.mbine.org/author/combine-2023/) | 2023-10-5/8 | Farmington, CT, USA | | -| [HARMONY 2023](https://co.mbine.org/author/harmony-2023/) | 2023-04-24/27 | University of Washington, Seattle, WA, USA | | -| [COMBINE 2022](https://co.mbine.org/author/combine-2022/) | 2022-10-6/8 | Berlin, Germany | | -| [HARMONY 2022](/event/2022/harmony) | 2022-04-26/30 | Washington, DC and Hybrid | | -| [COMBINE 2021](/event/2021/combine) | 2021-10-11/15 | Online (virtual) | | -| [HARMONY 2021](/event/2021/harmony) | 2021-03-22/26 | Online (virtual) | | -| COMBINE 2020 | 2020-10-05/09 | UConn Health, Connecticut, USA | Slides | -| HARMONY 2020 | 2020-03-09/13 | EMBL-EBI, Cambridgeshire, UK | Slides | -| COMBINE 2019 & EU-STANDS4PM | 2019-07-15/19 | Studio Villa Bosch, Heidelberg, Germany | Slides | -| HARMONY 2019 | 2019-03-25/29 | Caltech, Pasadena, California, USA | | -| COMBINE 2018 | 2018-10-08/12 | Boston University in Boston, MA, USA | | -| HARMONY 2018 | 2018-06-18/22 | Oxford University, UK | Slides | -| COMBINE 2017 | 2017-10-09/13 | Università degli Studi di Milano Bicocca in Milan, Italy | Slides | -| HARMONY 2017 | 2017-06-26/30 | University of Washington in Seattle, WA, USA | Slides | -| COMBINE 2016 | 2016-09-19/24 | Newcastle University in Newcastle Upon Tyne, UK | Slides | -| SBOL 14 | 2016-03-14/16 | Raytheon BBN Technologies in Boston, MA, USA | Slides | -| COMBINE 2015 | 2015-10-12/16 | University of Utah in Salt Lake City, UT, USA | Slides | -| HARMONY 2015 | 2015-03-20 | Wittenberg, Germany, EU | | -| COMBINE 2014 | 2014-08-18/22 | University of Southern California in Los Angeles, CA, USA | Slides | -| SBOL 10 | 2014-01-07/09 | UC Berkeley, CA, USA | Slides | -| SBOL 9 | 2013-04-24/26 | Newcastle University in Newcastle, UK | Slides | -| SBOL 8 | 2012-11-07/08 | Boston University in Boston, MA, USA | Slides | -| SBOL 7 | 2012-06-05 | Marriot Courtyard in San Francisco, CA, USA | Slides | -| SBOL 6 | 2012-01-05/06 | Univeristy of Washington in Seattle, WA, USA | Slides | -| SBOL 5 | 2011-06-08 | The Omni Hotel in San Diego, CA, USA | | -| SBOL 4 | 2011-01-07 | The Inn at Virginia Tech in Blacksburg, VA, USA | | -| SBOL 3 | 2010-06-13 | Hilton Anaheim in Anaheim, CA, USA | | -| SBOL 2 | 2009-07-26 | Stanford University in Stanford, CA, USA | Slides | -| SBOL 1 | 2008-04-27 | University of Washington in WA, USA | Programme | +outreach: + - name: "IWBDA 2026" + type: "IWBDA" + date: "2026-06-18" + date_display: "Jun 2026" + location: "University of Colorado Boulder, CO, USA" + url: "/event/2026/iwbda" + - name: "IWBDA 2023" + type: "IWBDA" + date: "2023-09-01" + date_display: "Sep 2023" + location: "Boston, MA, USA" + url: "/event/2023/iwbda/" + - name: "SEED 2023" + type: "SEED" + date: "2023-05-01" + date_display: "May 2023" + location: "Los Angeles, CA, USA" + url: "/event/2023/seed/" + - name: "IWBDA 2022" + type: "IWBDA" + date: "2022-10-01" + date_display: "Oct 2022" + location: "Paris, France" + url: "/event/2022/iwbda/" + - name: "SEED 2022" + type: "SEED" + date: "2022-05-01" + date_display: "May 2022" + location: "Arlington, VA, USA" + url: "/event/2022/seed/" + - name: "IWBDA 2021" + type: "IWBDA" + date: "2021-09-01" + date_display: "Sep 2021" + location: "Virtual" + url: "/event/2021/iwbda/" + - name: "SEED 2021" + type: "SEED" + date: "2021-06-01" + date_display: "Jun 2021" + location: "Virtual" + url: "/event/2021/seed/" + - name: "IWBDA 2020" + type: "IWBDA" + date: "2020-06-01" + date_display: "Jun 2020" + location: "Worcester, MA, USA" + url: "https://www.iwbdaconf.org/2020/" + - name: "Software for SynBio Workflows" + type: "Workshop" + date: "2020-06-01" + date_display: "Jun 2020" + location: "San Francisco, CA, USA" + url: "http://synbioconference.org/2020/events/software-synthetic-biology-workflows-workshop" + - name: "IWBDA 2019" + type: "IWBDA" + date: "2019-07-01" + date_display: "Jul 2019" + location: "Cambridge, UK" + url: "/event/2019/iwbda/" + - name: "Software for SynBio Workflows" + type: "Workshop" + date: "2019-06-01" + date_display: "Jun 2019" + location: "New York, NY, USA" + url: "/event/2019/software-for-synthetic-biology-workflows/" + - name: "SEED 2019" + type: "SEED" + date: "2019-06-01" + date_display: "Jun 2019" + location: "New York City, NY, USA" + url: "/event/2019/seed/" + - name: "IWBDA 2018" + type: "IWBDA" + date: "2018-07-01" + date_display: "Jul 2018" + location: "Berkeley, CA, USA" + url: "/event/2018/iwbda/" + - name: "SEED 2018" + type: "SEED" + date: "2018-06-01" + date_display: "Jun 2018" + location: "Scottsdale, AZ, USA" + url: "https://synbioconference.org/2018" + - name: "IWBDA 2017" + type: "IWBDA" + date: "2017-08-01" + date_display: "Aug 2017" + location: "University of Pittsburgh, PA, USA" + url: "/event/2017/iwbda/" + - name: "SEED 2017" + type: "SEED" + date: "2017-06-01" + date_display: "Jun 2017" + location: "Vancouver, British Columbia, Canada" + url: "/event/2017/seed/" + - name: "SB7.0" + type: "SynBio Conf" + date: "2017-07-01" + date_display: "Jul 2017" + location: "National University of Singapore" + url: "/event/2017/sb7/" + - name: "Living Computing Project" + type: "Seminar" + date: "2017-05-01" + date_display: "May 2017" + location: "Boston University, MA, USA" + url: "/event/2017/lcp/" + - name: "EMBL-EBI" + type: "Seminar" + date: "2017-05-01" + date_display: "May 2017" + location: "European Bioinformatics Institute, Cambridge, UK" + url: "/event/2017/embl-ebi/" + - name: "iBioK" + type: "Seminar" + date: "2017-02-01" + date_display: "Feb 2017" + location: "Kobe University, Japan" + url: "/event/2017/ibiok/" + - name: "IET/SynbiCITE" + type: "Conference" + date: "2016-12-01" + date_display: "Dec 2016" + location: "London, UK" + url: "http://www.synbicite.com/news-events/events/iet-synbicite-engineering-biology-conference/" + - name: "IWBDA 2016" + type: "IWBDA" + date: "2016-08-01" + date_display: "Aug 2016" + location: "Newcastle upon Tyne, UK" + url: "https://www.iwbdaconf.org/2016/" + - name: "Nona" + type: "Seminar" + date: "2016-07-01" + date_display: "Jul 2016" + location: "Chicago, IL, USA" + url: "https://www.nonasoftware.org/events" + - name: "ISMB 2016" + type: "Conference" + date: "2016-07-01" + date_display: "Jul 2016" + location: "Orlando, FL, USA" + url: "https://www.iscb.org/ismb2016" + - name: "IWBDA 2015" + type: "IWBDA" + date: "2015-08-01" + date_display: "Aug 2015" + location: "University of Washington, WA, USA" + url: "/event/2015/iwbda/" + - name: "SEED 2015" + type: "SEED" + date: "2015-06-01" + date_display: "Jun 2015" + location: "Chicago, IL, USA" + url: "/event/2015/seed/" + - name: "ICSB 2014" + type: "Conference" + date: "2014-09-01" + date_display: "Sep 2014" + location: "Melbourne, Australia" + url: "/event/2014/icsb/" + - name: "SEED 2014" + type: "SEED" + date: "2014-07-01" + date_display: "Jul 2014" + location: "Manhattan Beach, CA, USA" + url: "/event/2014/seed/" + - name: "IWBDA 2014" + type: "IWBDA" + date: "2014-06-01" + date_display: "Jun 2014" + location: "Boston, MA, USA" + url: "/event/2014/iwbda/" + - name: "IWBDA 2013" + type: "IWBDA" + date: "2013-07-01" + date_display: "Jul 2013" + location: "Imperial College, London, UK" + url: "/event/2013/iwbda/" + - name: "SB6.0" + type: "SynBio Conf" + date: "2013-07-01" + date_display: "Jul 2013" + location: "Imperial College, London, UK" + url: "/event/2013/sb6/" + - name: "Soundbiolab" + type: "Seminar" + date_display: "" + location: "University of Washington, Seattle, WA, USA" + url: "/event/2018/soundbiolab/" +--- diff --git a/content/community/_index.md b/content/community/_index.md index 3d68da848..23aab7fa9 100644 --- a/content/community/_index.md +++ b/content/community/_index.md @@ -19,198 +19,3 @@ The SBOL community works actively on the SBOL data model and visual standard, pa To join our growing community, contact the SBOL Editors [here](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit). - -### Members - -| Name | Affiliation | Country | -|----------------------------|-----------------------------------------------------------|-----------------| -| Abby Moore | University of Georgia | USA | -| AJ Abam | Colorado University, Boulder | USA | -| Alex McFadden | Zymergen Inc | USA | -| Alexis Casas | Imperial College London | UK | -| Alice Boo | Imperial College London | UK | -| Ana Delgado | University of Oslo | Norway | -| Angel Goñi-Moreno | Newcastle University | UK | -| Anil Wipat | Newcastle University | UK | -| Anton Kulaga | Computation Biology of Aging Group | Romania | -| Augustin Luna | Dana-Farber Cancer Institute | USA | -| Benjamin Aleritsch | Technical University of Munich | Germany | -| Benjamin Chan | Boston University | USA | -| Bill Yang | Newcastle University | UK | -| Birjesh Kumar | ICGEB, Delhi | India | -| Brad Chapman | Ginkgo Bioworks | USA | -| Brigitte Dreger | BioRender Inc. | Toronto | -| Bryan Bartley | BBN Technologies | USA | -| Bryan Der | MIT | USA | -| Carlog Olguin | Autodesk | USA | -| Carlos Vidal | University of Chile | Chile | -| Cesar Puentes | Independent | Columbia | -| Cesar Rodriguez | Florida State University | USA | -| Chih-Hsien Yang | National Yang Ming University | Taiwan | -| Chris Anderson | University of California, Berkeley | USA | -| Chris Myers | University of Colorado | USA | -| Chris Walker | Macquarie University | Australia | -| Christian Atallah | Newcastle University | UK | -| Christian Nyumbayire | Independent | Italy | -| Christian Olsen | Centers for Disease Control and Prevention | USA | -| Christopher Voigt | MIT | USA | -| Craig Struble | Inscripta Inc. | USA | -| Curtis Madsen | Sandia National Laboratories | USA | -| DA Ball | University of Tennessee | USA | -| Daniel Dixon | University of Bristol | UK | -| Daniel Sutantyo | Macquarie University | USA | -| Dany Entezari | University of Edinburgh | UAE | -| Darren Platt | Amyris | USA | -| David Lomelin | Synthetic Genomics | USA | -| David Ross | NIST | USA | -| David Zong | Rice University | USA | -| Douglas Densmore | Boston University | USA | -| Drew Endy | Stanford University & BIOFAB | USA | -| Eduardo Abeliuk | Teselagen | USA | -| Egils Stalidzans | University of Latvia | Latvia | -| Elizabeth Robinson | UT Austin | USA | -| Elizabeth Strychalsky | NIST | USA | -| Emek Demir | Memorial Sloan Kettering Cancer Center | USA | -| Eric van der Helm | SNIPRBIOME | Denmark | -| Eric Young | Worchester Polytechnic Institute | USA | -| Ernst Oberortner | Lawrence Berkeley National Labs | USA | -| Evan Appleton | Boston University | USA | -| Evren Sirin | Clark & Parsia | USA | -| Falk Schreiber | University of Konstanz | Germany | -| Falk Shreiber | University of Konstanz | Germany | -| Florencio Mazzoldi | Ginkgo Bioworks | USA | -| Gary Bader | University of Toronto | Canada | -| Ge Xiao Yu | Nanyang Technological University | Singapore | -| Geoff Baldwin | Imperial College London | USA | -| George McArthur | GenoCAD | USA | -| Göksel Mısırlı | Keele University | UK | -| Gonzalo Vidal Pena | University of Chile | Chile | -| Grimaldo Elias Urena M. | Technological University of Panama | Panama | -| Guillermo Yanez Feliu | Rudge Lab, PUC. | Chile | -| Guy Bart-Stan | Imperial College London | UK | -| Harold Fellermann | Newcastle University | UK | -| Hasan Baig | Independent | Pakistan | -| Hasan Baig | University of Connecticut | USA | -| Haseong Kim | Korea Research Institute of Bioscience and Biotechnology| South Korea | -| Hector Plahar | Joint Bioenergy Institute (JBEI) | USA | -| Henry Holbrook | Benchling | USA | -| Herbert Sauro | University of Washington | USA | -| Hiroyuki Kuwahara | KAUST | Saudi Arabia | -| Huaiyu Mi | USC | USA | -| Igor Durovic | Google | USA | -| Isabel Pötzsch | University of Cambridge | UK | -| Jackie Quinn | Google | USA | -| Jake Beal | BBN Technologies | USA | -| Jake Sumner | Keele University | UK | -| James Diggans | Twist Bioscience | USA | -| James McLaughlin | EMBL-EBI | UK | -| James Scholz | Genetic Logic Lab | USA | -| James Scott Brown | Imperial College London | UK | -| James Skelton | Newcastle University | UK | -| Jan Madsen | DTU | Denmark | -| Jared Earl | Forcepoint | USA | -| Jason Mohabir | Columbia University | USA | -| Jasper Koehorst | Wageningen University | Netherlands | -| Jean Peccoud | Colorado State University | USA | -| Jeanet Mante | University of Colorado | USA | -| Jeffrey Barrick | UT Austin | USA | -| Jeffrey Elhai | Virginia Commonwealth University | USA | -| Jenhan Tao | University of California, San Diego | USA | -| Jennifer Hallinan | Macquarie University | Australia | -| John Gennari | University of Washington | USA | -| John Meng | Lawrence Berkeley National Labs | USA | -| John T. Sexton | Independent | USA | -| Jonathan Karr | Mount Sinai | USA | -| Joseph Hellerstein | University of Washington | USA | -| Joshua Rawlins | UW-Madison | USA | -| Juston Farlow | Serotiny | USA | -| Jyotsna Venkata | St. Joseph's Institute of Technology | India | -| Kelvin Clancy | BioCoder Consulting | USA | -| Kevin Clancy | BioCoder Consulting | USA | -| Kiri Choi | University of Washington | USA | -| Kirtan Dave | Sardar Patel University | India | -| Kyle Medley | University of Washington | USA | -| Laura Adam | Virginia Bioinformatics Institute | USA | -| Linda Kahl | Stanford University | USA | -| Linh Huynh | UC Davis | USA | -| Linhao Meng | Zhejiang University | China | -| Lukas Buecherl | Colorado University, Boulder | USA | -| Maciek Jacek Swat | CSIRO | Australia | -| Mandy Wilson | Virginia Tech | USA | -| Marc Juul | BIOFAB | USA | -| Marco Castelejin | VTT Technical Research Centre | Finland | -| Mario Marchiso | Tianjin University | China | -| Marta Vazquez-Vilar | CSIC (Consejo Superior de Investigaciones Científicas) | Spain | -| Matthew Crowther | Newcastle University | UK | -| Matthew Lux | Army Research Lab | USA | -| Matthew Pocock | Newcastle University | UK | -| Matthieu Bultelle | Imperial College London | UK | -| Maurice Ling | AdvanceSyn Private Limited | Singapore | -| Maxwell Bates | Autodesk | USA | -| Meher Samineni | REI | USA | -| Michael Zhang | Google | USA | -| Michal Galdzicki | Arzeda | USA | -| Michihiro Araki | Kobe University | Japan | -| Mike Bissell | Shipyard Toolchains | USA | -| Mike Fero | Teselagen | USA | -| Nathan Hillson | Joint Bioenergy Institute | USA | -| Nathan Wilkinson | Recursion Pharmaceuticals | USA | -| Neil Swainston | Manchester BioFactory Ltd. | UK | -| Neil Thompson | Massachusetts Institute of Technology | USA | -| Nicholas Roehner | BBN Technologies | USA | -| Nicolas Le Novere | EMBL-EBI | UK | -| Noah Sprent | Imperial College | UK | -| Owen Gilfellon | Newcastle University | UK | -| Pablo Carbonell | Manchester Institute of Biotechnology | USA | -| Patrick Yizhi | University of Edinburgh | UK | -| Payton J Thomas | University of Utah | USA | -| Pedro Fontanarrosa | University of Utah | USA | -| Peter Dun | Stanford University | USA | -| Philip Bradley | Newcastle University | UK | -| Prashant Vaidyanathan | Microsoft Inc. | UK | -| Prem Prakash | BITS Pilani | India | -| Rahmi Lale | NTNU | Norway | -| Raik Gruenberg | KAUST | Saudi Arabia | -| Richard Kitney | Imperial College London | UK | -| Robert Sidney Cox | Robert Sydney Cox III Co. | USA | -| Robin Emig | Augment Bioworks | USA | -| S. Castillo Hair | Rice University | USA | -| Sarah Munro | NIST | USA | -| Sean Leonard | University of Texas at Austin | USA | -| Shamseen Rahman | Boston University | USA | -| Shashank | IIT Delhi | India | -| Shyam Bhakta | UC Berkeley | USA | -| SSBSS Summer School | SSBSS Summer School | Italy | -| Stefan Claesen | Visbion Ltd. | UK | -| Stuart Moodie | Eight Pillars Ltd. | Edinburgh | -| Sunwoo Kang | Stanford University | USA | -| Swapnil Bhatiya | Catalog Inc | USA | -| Thomas Gorochowski | Bio Compute Lab, Bristol University | UK | -| Tim Fiori | University of Australia | Australia | -| Todd Slaby | Lawrence Berkeley National Labs | USA | -| Tramy Nguyen | BBN Technologies | USA | -| Tyler Camp | University of Texas at Austin | USA | -| Ueno Masayoshi | Kitasato University | Japan | -| Umesh P | University of Kerala | India | -| Vinod Tek | Imperial College London | UK | -| Vishvesh Kulkarni | University of Warwick | UK | -| Vittorio Bartoli | University of Bristol | UK | -| Walid El-Sharoud | Mansoura University | Egypt | -| William Byrd | University of Alabama | USA | -| Xin Gao | KAUST | Saudi Arabia | -| Xuefeng Cui | University of Washington | USA | -| Yaman Sirin | BBN Technologies | USA | -| Yogev Debbi | Genome Compiler | USA | -| Ysis Tarter | Amyris | USA | -| Zach Palchick | Zymergen | USA | -| Zach Zundel | Facebook | USA | -| Zhen Zhang | Utah State University | USA | -| Zhiyang Ong | Texas A&M University | USA | -| Mudasir Shaikh | Habib University | Pakistan | -| Ritwik Agarwal | Iiit Hyderabad | India | -| Ming Hia | Imperial College | UK | -| Zhiyang Ong | Texas A&M University | USA | -| Ana Delgado | University of Oslo | Norway | -| William Poole | Caltech | USA | -| Stephanie Nicole Call | University of Massachusetts Amherst | USA | -| Gurvinder Dahiya | Independent | Norway | diff --git a/content/developer/_index.md b/content/developer/_index.md new file mode 100644 index 000000000..6e301c9ff --- /dev/null +++ b/content/developer/_index.md @@ -0,0 +1,73 @@ +--- +title: "SBOL for Developers" +subtitle: "A precise data model, official libraries in multiple languages, and an active open-source community. Everything you need to build SBOL-native tools." + +benefits: + - icon: "fas fa-book" + title: "Formal Specification" + description: "A rigorously defined data model backed by an OWL ontology - unambiguous enough to implement against with confidence." + - icon: "fas fa-code" + title: "Multi-language Libraries" + description: "Official implementations in Python, Java, JavaScript, C++, and more - pick the one that fits your stack." + - icon: "fas fa-plug" + title: "Open Toolchain" + description: "Validator, converter, and repository APIs ready to integrate into your pipeline or application." + +libraries_title: "Libraries" +libraries_description: "The SBOL community maintains official libraries across multiple languages. Whether you are working in Python, Java, JavaScript, C++, or F#, there is a library ready for your stack. All libraries implement the SBOL Core data model and are open-source." +libraries_url: "/libraries" +libraries_languages: + - "Python" + - "Java" + - "JavaScript" + - "C++" + - "F#" + +spec_title: "The Specification" +spec_description: "Everything a developer needs to implement SBOL correctly - the full data model, class definitions, validation rules, and the underlying OWL ontology." +spec_links: + - label: "Data Model Specification" + description: "Full class definitions and validation rules" + icon: "fas fa-file-alt" + url: "/DataModel-Specification" + - label: "Visual Specification" + description: "Standard for diagrammatic representation of designs" + icon: "fas fa-pencil-ruler" + url: "/visual-specification" + - label: "SBOL Ontology" + description: "OWL ontology for semantic interoperability" + icon: "fas fa-project-diagram" + url: "/ontology" + +toolchain_title: "Toolchain" +toolchain_description: "Production-ready tools you can integrate directly into your application or pipeline." +toolchain_links: + - label: "Validator" + description: "Check SBOL documents for compliance" + icon: "fas fa-check-circle" + url: "https://validator.sbolstandard.org/" + - label: "Converter" + description: "Convert between SBOL 2, SBOL 3, and GenBank" + icon: "fas fa-exchange-alt" + url: "https://converter.sbolstandard.org/" + - label: "SynBioHub" + description: "Repository with a REST API for programmatic access" + icon: "fas fa-database" + url: "https://synbiohub.org" + +genai_title: "Understand the Spec Faster with AI" +genai_description: "Our SBOL GPT assistants are trained on the SBOL 2 and SBOL 3 specifications and their primary Python libraries. Use them to explore edge cases, understand class relationships, or get quick answers while you implement." +genai_url: "/genai-tools" + +contribute_title: "Get Involved" +contribute_description: "SBOL is developed entirely in the open. Browse the source, file issues, propose enhancements via SEPs, or join the conversation on the mailing list." +contribute_links: + - label: "GitHub" + description: "Source code, SEPs, and issue tracking" + icon: "fab fa-github" + url: "https://github.com/SynBioDex" + - label: "Mailing List" + description: "Developer discussions and announcements" + icon: "fas fa-envelope" + url: "https://groups.google.com/g/sbol-dev" +--- diff --git a/content/event/2026/iwbda/index.md b/content/event/2026/iwbda/index.md new file mode 100644 index 000000000..98646a1ab --- /dev/null +++ b/content/event/2026/iwbda/index.md @@ -0,0 +1,16 @@ +--- +title: IWBDA 2026 +date: 2026-06-08T00:00:00+00:00 +layout: post +permalink: /iwbda-2026/ +categories: + - Announcements +--- + +## Location: University of Colorado Boulder, Boulder, CO, USA + +## Dates: June 13 – 20, 2026 + +Tutorials: June 13–14  |  Main Workshop: June 18–20 + +## Link: diff --git a/content/genai-tools/_index.md b/content/genai-tools/_index.md new file mode 100644 index 000000000..0cbc5a14d --- /dev/null +++ b/content/genai-tools/_index.md @@ -0,0 +1,4 @@ +--- +title: "GenAI Tools" +subtitle: "AI-powered tools and assistants built around the SBOL standard. These resources can help you explore specifications, write SBOL documents, and learn the standard faster." +--- diff --git a/content/genai-tools/sbol2-gpt/index.md b/content/genai-tools/sbol2-gpt/index.md new file mode 100644 index 000000000..939e928aa --- /dev/null +++ b/content/genai-tools/sbol2-gpt/index.md @@ -0,0 +1,7 @@ +--- +title: "SBOL 2 GPT" +summary: "A custom ChatGPT assistant trained on the SBOL 2 specification and the pySBOL2 library. Ask it anything about SBOL 2 data models, syntax, and Python usage." +external_url: "https://chatgpt.com/g/g-dcSB4tQIA-sbol-2" +platform: "ChatGPT" +sbol_version: "2" +--- diff --git a/content/genai-tools/sbol3-gpt/index.md b/content/genai-tools/sbol3-gpt/index.md new file mode 100644 index 000000000..303b8096b --- /dev/null +++ b/content/genai-tools/sbol3-gpt/index.md @@ -0,0 +1,7 @@ +--- +title: "SBOL 3 GPT" +summary: "A custom ChatGPT assistant trained on the SBOL 3 specification and the pySBOL3 library. Ask it anything about SBOL 3 data models, syntax, and Python usage." +external_url: "https://chatgpt.com/g/g-FcRCPqKq6-sbol-3" +platform: "ChatGPT" +sbol_version: "3" +--- diff --git a/content/home/about.md b/content/home/about.md index d01a8a5e8..d29c3454b 100644 --- a/content/home/about.md +++ b/content/home/about.md @@ -2,7 +2,7 @@ # About widget. widget = "about" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 20 # Order that this section will appear in. title = "" diff --git a/content/home/applications.md b/content/home/applications.md index aba4fac23..ec7ea71b6 100644 --- a/content/home/applications.md +++ b/content/home/applications.md @@ -2,7 +2,7 @@ # A Projects section created with the Portfolio widget. widget = "portfolio" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 140 # Order that this section will appear. title = "SBOL Tools & Applications" diff --git a/content/home/featured.md b/content/home/featured.md index 7c74def83..e1e85d5cf 100644 --- a/content/home/featured.md +++ b/content/home/featured.md @@ -5,7 +5,7 @@ widget = "featured" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 80 # Order that this section will appear. title = "Featured Publications" diff --git a/content/home/get-started.md b/content/home/get-started.md new file mode 100644 index 000000000..8ae5a75ec --- /dev/null +++ b/content/home/get-started.md @@ -0,0 +1,25 @@ ++++ +widget = "blank" +headless = true +active = true +weight = 15 + +title = "" +subtitle = "" + +[design] + columns = "1" + +[design.background] + color = "white" + +[advanced] + css_class = "" ++++ + +{{< journey-cards >}} + {{< card title="For Biologists" image="/media/welcome/sbol_biologist.png" link="/biologist/" >}} + {{< card title="For Developers" image="/media/welcome/sbol_developer.png" link="/developer/" >}} + {{< card title="Join the Community" image="/media/welcome/sbol_join.png" link="/join/" >}} +{{< /journey-cards >}} + diff --git a/content/home/libraries.md b/content/home/libraries.md index 74718c311..aaa2599dc 100644 --- a/content/home/libraries.md +++ b/content/home/libraries.md @@ -2,7 +2,7 @@ # A Projects section created with the Portfolio widget. widget = "portfolio" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 65 # Order that this section will appear. title = "SBOL for developers!" diff --git a/content/home/sbol.md b/content/home/sbol.md index d9b644de6..c447d9976 100644 --- a/content/home/sbol.md +++ b/content/home/sbol.md @@ -1,85 +1,32 @@ +++ -# A Projects section created with the Portfolio widget. -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = true # Activate this widget? true/false -weight = 25 # Order that this section will appear. +widget = "blank" +headless = true +active = true +weight = 10 -title = "What is SBOL?" +title = "" subtitle = "" -[content] - # Page type to display. E.g. project. - page_type = "about" - - # Filter toolbar (optional). - # Add or remove as many filters (`[[content.filter_button]]` instances) as you like. - # To show all items, set `tag` to "*". - # To filter by a specific tag, set `tag` to an existing tag name. - # To remove toolbar, delete/comment all instances of `[[content.filter_button]]` below. - - # Default filter index (e.g. 0 corresponds to the first `[[filter_button]]` instance below). - filter_default = 0 - - # [[content.filter_button]] - # name = "All" - # tag = "*" - - # [[content.filter_button]] - # name = "Deep Learning" - # tag = "Deep Learning" - - # [[content.filter_button]] - # name = "Other" - # tag = "Demo" - [design] - - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "2" - - # Toggle between the various page layout types. - # 1 = List - # 2 = Compact - # 3 = Card - # 5 = Showcase - view = 5 - - # For Showcase view, flip alternate rows? - flip_alt_rows = false + columns = "1" [design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "navy" - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "background.jpg" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. + color = "white" - # Text color (true=light or false=dark). - # text_color_light = true - -[advanced] - # Custom CSS. - css_style = "" - - # CSS class. - css_class = "" - -# Commenting this section out. This can be used if we want a shorter description. -# The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. +[design.spacing] + padding = ["20px", "0", "20px", "0"] +[advanced] + css_class = "" +++ -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -You can learn more about SBOL by reading the [SBOL Data Model](/datamodel-about/) page. \ No newline at end of file +{{< hero-feed + badge="" + title="One language for every biological design." + subtitle="Developed by the synthetic biology community, SBOL is the free, open-source standard for representing biological designs. It provides a powerful, standardized format to seamlessly exchange structural and functional information, making your research more efficient and reproducible." + btn1_text="Get Started" + btn1_link="#get-started" + btn2_text="Join us on Slack" + btn2_link="https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg" + btn2_icon="fab fa-slack" +>}} diff --git a/content/home/specifications.md b/content/home/specifications.md index 3782e9671..6cd55c2e4 100644 --- a/content/home/specifications.md +++ b/content/home/specifications.md @@ -2,7 +2,7 @@ # A Projects section created with the Portfolio widget. widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 40 # Order that this section will appear. title = "Latest SBOL Specifications" diff --git a/content/home/visual.md b/content/home/visual.md index 56aadb52a..f41aac5ed 100644 --- a/content/home/visual.md +++ b/content/home/visual.md @@ -2,7 +2,7 @@ # A Projects section created with the Portfolio widget. widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 30 # Order that this section will appear. title = "Visualize with SBOL Visual!" diff --git a/content/home/voices.md b/content/home/voices.md new file mode 100644 index 000000000..f7efb9880 --- /dev/null +++ b/content/home/voices.md @@ -0,0 +1,17 @@ ++++ +widget = "pages" +headless = true +active = true +weight = 90 + +title = "Voices from the Community" +subtitle = "Insights and updates directly from the developers and users." + +[content] + page_type = "blog" + count = 3 + order = "desc" + +[design] + view = 3 ++++ diff --git a/content/join/_index.md b/content/join/_index.md new file mode 100644 index 000000000..42f27759b --- /dev/null +++ b/content/join/_index.md @@ -0,0 +1,71 @@ +--- +title: "Join the SBOL Community" +subtitle: "SBOL is built by the community, for the community. Whether you contribute code, attend workshops, or simply stay informed - there is a place for you." + +reasons: + - icon: "fas fa-pen-nib" + title: "Shape the Standard" + description: "SEPs (SBOL Enhancement Proposals) and working groups are open to all. Your use case and feedback directly influence the next version." + - icon: "fas fa-globe" + title: "Connect Globally" + description: "Researchers from academia, industry, and government across 17 countries working together on a shared language for biology." + - icon: "fas fa-lock-open" + title: "Open by Default" + description: "All discussions happen in public. No gatekeeping, no membership fee - just a shared commitment to better science." + +stats: + - number: "170+" + label: "Members" + - number: "17" + label: "Countries" + - number: "42" + label: "Institutions" + - number: "28" + label: "Industries" + +stats_note: "Our members are also active in related standards communities including the Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN)." + +connect_title: "Ways to Get Involved" +connect_links: + - label: "Join us on Slack" + description: "Chat with the community in real time" + icon: "fab fa-slack" + url: "https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg" + - label: "Mailing List" + description: "Stay informed on announcements and discussions" + icon: "fas fa-envelope" + url: "https://groups.google.com/g/sbol-announce" + - label: "GitHub" + description: "Contribute code, file issues, and propose SEPs" + icon: "fab fa-github" + url: "https://github.com/SynBioDex" + - label: "Formal Membership" + description: "Fill in our form to officially join the community" + icon: "fas fa-user-plus" + url: "https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit" + +meetings_title: "Attend a Meeting" +meetings_description: "The SBOL community meets semi-annually at COMBINE and HARMONY workshops, and engages the broader synthetic biology community at conferences worldwide. All meetings are open to attend." +meetings_url: "/community-meetings" + +structure_title: "How We Are Organised" +structure_description: "SBOL is governed by a steering committee of elected members and managed by a chair and editors who oversee the standard." +structure_links: + - label: "Leadership" + description: "Chair, editors, and steering committee" + icon: "fas fa-users" + url: "/community-leadership" + - label: "Governance" + description: "How decisions are made" + icon: "fas fa-balance-scale" + url: "/community-governance" + - label: "SBOL Industrial Consortium" + description: "Industry participation in the standard" + icon: "fas fa-industry" + url: "/sbol-industrial" + +cta_title: "Ready to Join?" +cta_description: "Fill in our membership form and we will be in touch. No obligations - just a way for us to know you are part of the community." +cta_btn_text: "Join the Community" +cta_btn_url: "https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit" +--- diff --git a/content/libraries/_index.md b/content/libraries/_index.md index 77c6abe90..24a76c4ee 100644 --- a/content/libraries/_index.md +++ b/content/libraries/_index.md @@ -1,27 +1,9 @@ --- title: Libraries - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" +subtitle: Community-contributed libraries implementing SBOL Core across languages and platforms. +tabs: +- id: "3" + label: "SBOL 3" +- id: "2" + label: "SBOL 2" --- - - -SBOL data is built off of the latest specification release and is available in C/C++, Java, JavaScript, Python, and F#. You can support the SBOL data model in your software tool by following the build instructions that are provided. A variety of software tools have reported that their tool support importing and exporting of the SBOL data model. Take a look at the latest software tools that support SBOL. Contact the library developers for further questions. - -Here's a list of links to the SBOL 3 libraries: - - -You can also access an exhaustive list of language specific libraries here: \ No newline at end of file diff --git a/content/libraries/sbol-notebooks/index.md b/content/libraries/sbol-notebooks/index.md new file mode 100644 index 000000000..f2feb2306 --- /dev/null +++ b/content/libraries/sbol-notebooks/index.md @@ -0,0 +1,14 @@ +--- +title: SBOL Notebooks +summary: Interactive Jupyter notebooks demonstrating data mapping, enrichment, and visualization for biological parts. +sbol_versions: ["2", "3"] +lib_category: resource +date: "2021-01-01T00:00:00Z" +links: +- icon: github + icon_pack: fab + name: Github + url: https://github.com/SynBioDex/SBOL-Notebooks +--- + +SBOL Notebooks is a collection of interactive Jupyter notebooks that demonstrate how to work with SBOL data, covering data mapping, enrichment, and visualization for biological parts. These notebooks are useful for both SBOL 2 and SBOL 3. diff --git a/content/libraries/sbol-utilities/index.md b/content/libraries/sbol-utilities/index.md new file mode 100644 index 000000000..7e2b189b6 --- /dev/null +++ b/content/libraries/sbol-utilities/index.md @@ -0,0 +1,14 @@ +--- +title: SBOL Utilities +summary: Command-line tools for conversion between GenBank, FASTA, and SBOL, plus structural validation. +sbol_versions: ["2", "3"] +lib_category: resource +date: "2021-01-01T00:00:01Z" +links: +- icon: github + icon_pack: fab + name: Github + url: https://github.com/SynBioDex/SBOL-utilities +--- + +A developer toolkit for SBOL 2 and SBOL 3 providing format conversion between Excel, GenBank, FASTA, and SBOL, alongside validation and utility functions for working with SBOL documents. \ No newline at end of file diff --git a/content/libraries/cpp/featured.png b/content/libraries/sbol2-cpp/featured.png similarity index 100% rename from content/libraries/cpp/featured.png rename to content/libraries/sbol2-cpp/featured.png diff --git a/content/libraries/cpp/index.md b/content/libraries/sbol2-cpp/index.md similarity index 97% rename from content/libraries/cpp/index.md rename to content/libraries/sbol2-cpp/index.md index 2b0c79946..435d4ae44 100644 --- a/content/libraries/cpp/index.md +++ b/content/libraries/sbol2-cpp/index.md @@ -3,6 +3,8 @@ title: C++ summary: Core C/C++ interfaces and implementations for SBOL tags: - Libraries +sbol_versions: ["2"] +lib_category: library date: "2018-01-01T00:00:01Z" # Optional external URL for project (replaces project detail page). diff --git a/content/libraries/fsharp/featured.png b/content/libraries/sbol2-fsharp/featured.png similarity index 100% rename from content/libraries/fsharp/featured.png rename to content/libraries/sbol2-fsharp/featured.png diff --git a/content/libraries/fsharp/index.md b/content/libraries/sbol2-fsharp/index.md similarity index 92% rename from content/libraries/fsharp/index.md rename to content/libraries/sbol2-fsharp/index.md index f4767f525..86ace0f68 100644 --- a/content/libraries/fsharp/index.md +++ b/content/libraries/sbol2-fsharp/index.md @@ -1,8 +1,10 @@ --- -title: F# -summary: F# libraries for SBOL +title: F Sharp +summary: F# libraries for SBOL 2 tags: - Libraries +sbol_versions: ["2"] +lib_category: library date: "2018-01-01T00:00:00Z" # Optional external URL for project (replaces project detail page). diff --git a/content/libraries/java/sbol2/_index.md b/content/libraries/sbol2-java/_index.md similarity index 97% rename from content/libraries/java/sbol2/_index.md rename to content/libraries/sbol2-java/_index.md index 6a98e2c65..8899d09fa 100644 --- a/content/libraries/java/sbol2/_index.md +++ b/content/libraries/sbol2-java/_index.md @@ -1,6 +1,9 @@ --- -title: libSBOLj +title: Java summary: Java interfaces and implementations for SBOL2 +sbol_versions: +- "2" +lib_category: primary tags: - Libraries date: "2018-01-01T00:00:02Z" @@ -31,7 +34,7 @@ links: url: docs/libsbolj_install.pdf - icon: code icon_pack: fas - name: Release (v 2.4.0) + name: Release url: https://github.com/SynBioDex/libSBOLj/releases - icon: bug icon_pack: fas diff --git a/content/libraries/java/featured.png b/content/libraries/sbol2-java/featured.png similarity index 100% rename from content/libraries/java/featured.png rename to content/libraries/sbol2-java/featured.png diff --git a/content/libraries/javascript/featured.jpg b/content/libraries/sbol2-js/featured.jpg similarity index 100% rename from content/libraries/javascript/featured.jpg rename to content/libraries/sbol2-js/featured.jpg diff --git a/content/libraries/javascript/index.md b/content/libraries/sbol2-js/index.md similarity index 98% rename from content/libraries/javascript/index.md rename to content/libraries/sbol2-js/index.md index 5bc11bff5..8049203bd 100644 --- a/content/libraries/javascript/index.md +++ b/content/libraries/sbol2-js/index.md @@ -3,6 +3,8 @@ title: JavaScript summary: Core JavaScript interfaces and implementations for SBOL tags: - Libraries +sbol_versions: ["2"] +lib_category: primary date: "2018-01-01T00:00:03Z" # Optional external URL for project (replaces project detail page). diff --git a/content/libraries/python/pysbol2/_index.md b/content/libraries/sbol2-py/_index.md similarity index 97% rename from content/libraries/python/pysbol2/_index.md rename to content/libraries/sbol2-py/_index.md index 4c12db688..14e2b2151 100644 --- a/content/libraries/python/pysbol2/_index.md +++ b/content/libraries/sbol2-py/_index.md @@ -1,6 +1,9 @@ --- -title: pySBOL2 +title: Python summary: Python interfaces and implementations for SBOL 2 +sbol_versions: +- "2" +lib_category: primary tags: - Libraries/Python date: "2018-01-01T00:00:04Z" diff --git a/content/libraries/python/featured.png b/content/libraries/sbol2-py/featured.png similarity index 100% rename from content/libraries/python/featured.png rename to content/libraries/sbol2-py/featured.png diff --git a/content/libraries/java/sbol2/featured.png b/content/libraries/sbol3-java/featured.png similarity index 100% rename from content/libraries/java/sbol2/featured.png rename to content/libraries/sbol3-java/featured.png diff --git a/content/libraries/java/index.md b/content/libraries/sbol3-java/index.md similarity index 97% rename from content/libraries/java/index.md rename to content/libraries/sbol3-java/index.md index e99c892d4..5109cd62e 100644 --- a/content/libraries/java/index.md +++ b/content/libraries/sbol3-java/index.md @@ -3,6 +3,8 @@ title: Java summary: Java interfaces and implementations for SBOL tags: - Libraries +sbol_versions: ["3"] +lib_category: primary date: "2023-05-10T00:00:02Z" # Optional external URL for project (replaces project detail page). @@ -68,6 +70,3 @@ N-Triples, and JSON-LD graph formats. The library also provides a higher-level API to abstract commonly used methods and a validator to programmatically validate SBOL documents or individual entities. - -# Older Versions -- [libSBOLj for SBOL2](sbol2) diff --git a/content/libraries/python/pysbol2/featured.png b/content/libraries/sbol3-py/featured.png similarity index 100% rename from content/libraries/python/pysbol2/featured.png rename to content/libraries/sbol3-py/featured.png diff --git a/content/libraries/python/index.md b/content/libraries/sbol3-py/index.md similarity index 98% rename from content/libraries/python/index.md rename to content/libraries/sbol3-py/index.md index 09647f327..07f4c9b06 100644 --- a/content/libraries/python/index.md +++ b/content/libraries/sbol3-py/index.md @@ -3,6 +3,8 @@ title: Python summary: Python interfaces and implementations for SBOL tags: - Libraries +sbol_versions: ["3"] +lib_category: primary date: "2022-02-15T16:30:18Z" # Optional external URL for project (replaces project detail page). diff --git a/content/post/_index.md b/content/post/_index.md index 5ba086fff..c28ec9c23 100644 --- a/content/post/_index.md +++ b/content/post/_index.md @@ -1,5 +1,5 @@ --- -title: Posts +title: Announcements # View. # 1 = List diff --git a/content/post/combine-2026/index.md b/content/post/combine-2026/index.md new file mode 100644 index 000000000..5e3e147f2 --- /dev/null +++ b/content/post/combine-2026/index.md @@ -0,0 +1,62 @@ +--- +title: "COMBINE 2026 — Workshop at Keele University, UK" +date: 2026-05-09 +summary: > + The 2026 COMBINE Workshop will be held at Keele University, UK, from + 7–10 September 2026. Registration and abstract submission are now open. +tags: + - Events + - COMBINE + - Community +--- + +The **Computational Modeling in Biology Network (COMBINE)** is an initiative to coordinate the development of community standards and formats in systems biology, synthetic biology, and related fields. + +**COMBINE 2026** will be hosted at Keele University, UK, from **7–10 September 2026**. The workshop includes talks, tutorials, and breakout sessions for detailed discussions about standards, related efforts, and tools. + +Full details — including venue, travel, and accommodation — are available at [co.mbine.org/events](https://co.mbine.org/events/). + +--- + +## Registration + +Registration is now open. In-person attendance requires a two-step process: first complete the Google form, then pay the registration fee via the Keele University website. + +--- + +## Abstract Submission + +Submissions are open for: + +- Talks +- Tutorials +- Breakout sessions +- Lightning talks +- Posters + +--- + +## Important Dates + +| Milestone | Date | +|---|---| +| Submission deadline (all categories) | 19 July 2026 | +| Notification of acceptance | 26 July 2026 | +| Registration deadline | 2 August 2026 | +| Late registration deadline | 23 August 2026 | +| COMBINE 2026 | 7–10 September 2026 | + +--- + +## Topics of Interest + +- Data exchange, pipelines, and model standards for systems and synthetic biology +- Visualization and graphical notation standards for systems and synthetic biology +- Standards for sharing and analyzing biological pathway data +- Standards for computational biological models and modeling support +- Metadata description and model annotation in COMBINE standard formats +- Implementation of COMBINE standards in tools, databases, and other resources +- Integrated model and data management for systems and synthetic biology +- Standardization of Artificial Intelligence approaches in biological modeling +- Emerging standardization needs and multicellular modeling +- Community aspects of COMBINE diff --git a/content/sponsor-sbol/_index.md b/content/sponsor-sbol/_index.md new file mode 100644 index 000000000..3e795c464 --- /dev/null +++ b/content/sponsor-sbol/_index.md @@ -0,0 +1,36 @@ +--- +title: Support SBOL +subtitle: "SBOL is a free, open standard maintained by a global volunteer community. Supporting the Bio-Design Automation Consortium (BDAC) is how you help keep SBOL active, visible, and growing." + +bdac_url: "https://bio-design-automation.org" + +benefits: + - icon: "fas fa-chalkboard-teacher" + title: "Logo in Presentations" + body: "Your organization's logo will appear in all SBOL presentations at major workshops and conferences, including IWBDA, COMBINE, and HARMONY." + - icon: "fas fa-globe" + title: "Website Recognition" + body: "Your logo will be featured on the SBOL website as a recognized supporter of the standard." + - icon: "fas fa-bullhorn" + title: "Community Announcements" + body: "Recognition in SBOL community communications, including our mailing list and Slack workspace." + - icon: "fas fa-users" + title: "Steering Committee Visibility" + body: "Supporters are invited to attend SBOL Steering Committee meetings as observers, with direct visibility into the direction of the standard." + +past_sponsors: + - name: "Raytheon BBN" + logo: "raytheon.jpeg" + - name: "Doulix" + logo: "doulix.png" + - name: "IDT" + logo: "idt.png" + - name: "Twist Bioscience" + logo: "Twist_Logo_cropped.jpeg" + - name: "Amyris" + logo: "amyris-1.png" + - name: "Inscripta" + logo: "Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" + - name: "Teselagen" + logo: "Teselagen_300x150-1.png" +--- diff --git a/content/visual-gallery/_index.md b/content/visual-gallery/_index.md new file mode 100644 index 000000000..af28a4b7a --- /dev/null +++ b/content/visual-gallery/_index.md @@ -0,0 +1,5 @@ +--- +title: SBOL Visual Gallery +subtitle: A showcase of beautiful SBOL Visual diagrams from published manuscripts. Click any image to view it in full and explore the original publication. +submit_url: "https://forms.gle/JVf211WTvj46vLRt8" +--- diff --git a/content/visual-gallery/sb-2015-00287k/cite.bib b/content/visual-gallery/sb-2015-00287k/cite.bib new file mode 100644 index 000000000..afb8cb3e8 --- /dev/null +++ b/content/visual-gallery/sb-2015-00287k/cite.bib @@ -0,0 +1,10 @@ +@article{kim2016cell, + title={A cell--cell communication-based screening system for novel microbes with target enzyme activities}, + author={Kim, Haseong and Rha, Eugene and Seong, Wonjae and Yeom, Soo-Jin and Lee, Dae-Hee and Lee, Seung-Goo}, + journal={ACS Synthetic Biology}, + volume={5}, + number={11}, + pages={1231--1238}, + year={2016}, + publisher={ACS Publications} +} \ No newline at end of file diff --git a/content/visual-gallery/sb-2015-00287k/images_large_sb-2015-00287k_0002.jpeg b/content/visual-gallery/sb-2015-00287k/images_large_sb-2015-00287k_0002.jpeg new file mode 100644 index 000000000..8fbd0178e Binary files /dev/null and b/content/visual-gallery/sb-2015-00287k/images_large_sb-2015-00287k_0002.jpeg differ diff --git a/content/visual-gallery/sb-2015-00287k/index.md b/content/visual-gallery/sb-2015-00287k/index.md new file mode 100644 index 000000000..0623e5965 --- /dev/null +++ b/content/visual-gallery/sb-2015-00287k/index.md @@ -0,0 +1,5 @@ +--- +title: "A cell-cell communication-based screening system for novel microbes with target enzyme activities" +doi: "10.1021/acssynbio.5b00287" +publication_url: "https://pubs.acs.org/doi/10.1021/acssynbio.5b00287" +--- diff --git a/content/visual-gallery/sb-2017-00212u/cite.bib b/content/visual-gallery/sb-2017-00212u/cite.bib new file mode 100644 index 000000000..0f548693a --- /dev/null +++ b/content/visual-gallery/sb-2017-00212u/cite.bib @@ -0,0 +1,10 @@ +@article{craig2017leaf, + title={Leaf LIMS: a flexible laboratory information management system with a synthetic biology focus}, + author={Craig, Thomas and Holland, Richard and D’Amore, Rosalinda and Johnson, James R and McCue, Hannah V and West, Anthony and Zulkower, Valentin and Tekotte, Hille and Cai, Yizhi and Swan, Daniel and others}, + journal={ACS synthetic biology}, + volume={6}, + number={12}, + pages={2273--2280}, + year={2017}, + publisher={ACS Publications} +} \ No newline at end of file diff --git a/content/visual-gallery/sb-2017-00212u/image.jpeg b/content/visual-gallery/sb-2017-00212u/image.jpeg new file mode 100644 index 000000000..e9e571874 Binary files /dev/null and b/content/visual-gallery/sb-2017-00212u/image.jpeg differ diff --git a/content/visual-gallery/sb-2017-00212u/index.md b/content/visual-gallery/sb-2017-00212u/index.md new file mode 100644 index 000000000..5c095994e --- /dev/null +++ b/content/visual-gallery/sb-2017-00212u/index.md @@ -0,0 +1,5 @@ +--- +title: "Leaf LIMS: a flexible laboratory information management system with a synthetic biology focus" +doi: "10.1021/acssynbio.7b00212" +publication_url: "https://pubs.acs.org/doi/10.1021/acssynbio.7b00212" +--- diff --git a/content/visual-gallery/sb1c00281/cite.bib b/content/visual-gallery/sb1c00281/cite.bib new file mode 100644 index 000000000..30f921aec --- /dev/null +++ b/content/visual-gallery/sb1c00281/cite.bib @@ -0,0 +1,10 @@ +@article{mcbride2021predicting, + title={Predicting composition of genetic circuits with resource competition: demand and sensitivity}, + author={McBride, Cameron D and Del Vecchio, Domitilla}, + journal={ACS Synthetic Biology}, + volume={10}, + number={12}, + pages={3330--3342}, + year={2021}, + publisher={ACS Publications} +} \ No newline at end of file diff --git a/content/visual-gallery/sb1c00281/image.jpeg b/content/visual-gallery/sb1c00281/image.jpeg new file mode 100644 index 000000000..0110095b6 Binary files /dev/null and b/content/visual-gallery/sb1c00281/image.jpeg differ diff --git a/content/visual-gallery/sb1c00281/index.md b/content/visual-gallery/sb1c00281/index.md new file mode 100644 index 000000000..eea8c7702 --- /dev/null +++ b/content/visual-gallery/sb1c00281/index.md @@ -0,0 +1,5 @@ +--- +title: "Predicting composition of genetic circuits with resource competition: demand and sensitivity" +doi: "10.1021/acssynbio.1c00281" +publication_url: "https://pubs.acs.org/doi/10.1021/acssynbio.1c00281" +--- diff --git a/content/visual-glyphs/_index.md b/content/visual-glyphs/_index.md deleted file mode 100644 index a4f81c074..000000000 --- a/content/visual-glyphs/_index.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### Glyphs - -Zip files containing images of the glyphs as PDF, PNG or SVG files can be downloaded from the [Releases page](https://github.com/SynBioDex/SBOL-visual/releases) of the SBOL Visual repository on GitHub. - - - - - - - - - - - - - - - - diff --git a/content/visual-glyphs/gallery/aptamer.png b/content/visual-glyphs/gallery/aptamer.png new file mode 100644 index 000000000..71027e0e0 Binary files /dev/null and b/content/visual-glyphs/gallery/aptamer.png differ diff --git a/content/visual-glyphs/gallery/aptamer.svg b/content/visual-glyphs/gallery/aptamer.svg new file mode 100644 index 000000000..ba31c04be --- /dev/null +++ b/content/visual-glyphs/gallery/aptamer.svg @@ -0,0 +1,53 @@ + + + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/assembly-scar.png b/content/visual-glyphs/gallery/assembly-scar.png new file mode 100644 index 000000000..1be25133f Binary files /dev/null and b/content/visual-glyphs/gallery/assembly-scar.png differ diff --git a/content/visual-glyphs/gallery/assembly-scar.svg b/content/visual-glyphs/gallery/assembly-scar.svg new file mode 100644 index 000000000..b57c17112 --- /dev/null +++ b/content/visual-glyphs/gallery/assembly-scar.svg @@ -0,0 +1,63 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/association.png b/content/visual-glyphs/gallery/association.png new file mode 100644 index 000000000..3de9545c7 Binary files /dev/null and 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b/content/visual-glyphs/gallery/cds-arrow.png new file mode 100644 index 000000000..2c060d123 Binary files /dev/null and b/content/visual-glyphs/gallery/cds-arrow.png differ diff --git a/content/visual-glyphs/gallery/cds-arrow.svg b/content/visual-glyphs/gallery/cds-arrow.svg new file mode 100644 index 000000000..c0325941c --- /dev/null +++ b/content/visual-glyphs/gallery/cds-arrow.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/cds.png b/content/visual-glyphs/gallery/cds.png new file mode 100644 index 000000000..15a88d4bf Binary files /dev/null and b/content/visual-glyphs/gallery/cds.png differ diff --git a/content/visual-glyphs/gallery/cds.svg b/content/visual-glyphs/gallery/cds.svg new file mode 100644 index 000000000..180778c63 --- /dev/null +++ b/content/visual-glyphs/gallery/cds.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/chromosomal-locus.png b/content/visual-glyphs/gallery/chromosomal-locus.png new file mode 100644 index 000000000..8fb4875c0 Binary files /dev/null and b/content/visual-glyphs/gallery/chromosomal-locus.png differ diff --git a/content/visual-glyphs/gallery/chromosomal-locus.svg b/content/visual-glyphs/gallery/chromosomal-locus.svg new file mode 100644 index 000000000..60db777bf --- /dev/null +++ b/content/visual-glyphs/gallery/chromosomal-locus.svg @@ -0,0 +1,78 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + + + diff --git a/content/visual-glyphs/gallery/circular-plasmid.png b/content/visual-glyphs/gallery/circular-plasmid.png new file mode 100644 index 000000000..eac55785f Binary files /dev/null and b/content/visual-glyphs/gallery/circular-plasmid.png differ diff --git a/content/visual-glyphs/gallery/circular-plasmid.svg b/content/visual-glyphs/gallery/circular-plasmid.svg new file mode 100644 index 000000000..dd0fa39bd --- /dev/null +++ b/content/visual-glyphs/gallery/circular-plasmid.svg @@ -0,0 +1,84 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + + + diff --git a/content/visual-glyphs/gallery/complex-sbgn.png b/content/visual-glyphs/gallery/complex-sbgn.png new file mode 100644 index 000000000..6bb3ee61d Binary files /dev/null and b/content/visual-glyphs/gallery/complex-sbgn.png differ diff --git a/content/visual-glyphs/gallery/complex-sbgn.svg b/content/visual-glyphs/gallery/complex-sbgn.svg new file mode 100644 index 000000000..359a4a854 --- /dev/null +++ b/content/visual-glyphs/gallery/complex-sbgn.svg @@ -0,0 +1,58 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/composite.png b/content/visual-glyphs/gallery/composite.png new file mode 100644 index 000000000..8e0ad13f0 Binary files /dev/null and b/content/visual-glyphs/gallery/composite.png differ diff --git a/content/visual-glyphs/gallery/composite.svg b/content/visual-glyphs/gallery/composite.svg new file mode 100644 index 000000000..a8a0100c6 --- /dev/null +++ b/content/visual-glyphs/gallery/composite.svg @@ -0,0 +1,102 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + diff --git a/content/visual-glyphs/gallery/control.png b/content/visual-glyphs/gallery/control.png new file mode 100644 index 000000000..5c63da949 Binary files /dev/null and b/content/visual-glyphs/gallery/control.png differ diff --git a/content/visual-glyphs/gallery/control.svg b/content/visual-glyphs/gallery/control.svg new file mode 100644 index 000000000..4b17236d3 --- /dev/null +++ b/content/visual-glyphs/gallery/control.svg @@ -0,0 +1,66 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/degradation.png b/content/visual-glyphs/gallery/degradation.png new file mode 100644 index 000000000..74f7e7d7c Binary files /dev/null and b/content/visual-glyphs/gallery/degradation.png differ diff --git a/content/visual-glyphs/gallery/degradation.svg b/content/visual-glyphs/gallery/degradation.svg new file mode 100644 index 000000000..6af0c6b82 --- /dev/null +++ b/content/visual-glyphs/gallery/degradation.svg @@ -0,0 +1,85 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/dissociation.png b/content/visual-glyphs/gallery/dissociation.png new file mode 100644 index 000000000..b4f3e4e9e Binary files /dev/null and b/content/visual-glyphs/gallery/dissociation.png differ diff --git a/content/visual-glyphs/gallery/dissociation.svg b/content/visual-glyphs/gallery/dissociation.svg new file mode 100644 index 000000000..d269f106e --- /dev/null +++ b/content/visual-glyphs/gallery/dissociation.svg @@ -0,0 +1,78 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/dna-stability-element.png b/content/visual-glyphs/gallery/dna-stability-element.png new file mode 100644 index 000000000..b371b92b7 Binary files /dev/null and b/content/visual-glyphs/gallery/dna-stability-element.png differ diff --git a/content/visual-glyphs/gallery/dna-stability-element.svg b/content/visual-glyphs/gallery/dna-stability-element.svg new file mode 100644 index 000000000..62568bf5e --- /dev/null +++ b/content/visual-glyphs/gallery/dna-stability-element.svg @@ -0,0 +1,65 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/dsNA.png b/content/visual-glyphs/gallery/dsNA.png new file mode 100644 index 000000000..17aa1f93e Binary files /dev/null and b/content/visual-glyphs/gallery/dsNA.png differ diff --git a/content/visual-glyphs/gallery/dsNA.svg b/content/visual-glyphs/gallery/dsNA.svg new file mode 100644 index 000000000..29f3a6601 --- /dev/null +++ b/content/visual-glyphs/gallery/dsNA.svg @@ -0,0 +1,550 @@ + +image/svg+xmlUntitled VisBOL DesignUntitled VisBOL DesignGenerated by the VisBOL design visualizer at http://visbol.org + + \ No newline at end of file diff --git a/content/visual-glyphs/gallery/engineered-region.png b/content/visual-glyphs/gallery/engineered-region.png new file mode 100644 index 000000000..bfe655413 Binary files /dev/null and b/content/visual-glyphs/gallery/engineered-region.png differ diff --git a/content/visual-glyphs/gallery/engineered-region.svg b/content/visual-glyphs/gallery/engineered-region.svg new file mode 100644 index 000000000..929ef29fa --- /dev/null +++ b/content/visual-glyphs/gallery/engineered-region.svg @@ -0,0 +1,56 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/five-prime-overhang.png b/content/visual-glyphs/gallery/five-prime-overhang.png new file mode 100644 index 000000000..e748408d5 Binary files /dev/null and b/content/visual-glyphs/gallery/five-prime-overhang.png differ diff --git a/content/visual-glyphs/gallery/five-prime-overhang.svg b/content/visual-glyphs/gallery/five-prime-overhang.svg new file mode 100644 index 000000000..52720da68 --- /dev/null +++ b/content/visual-glyphs/gallery/five-prime-overhang.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/five-prime-sticky-restriction-site.png b/content/visual-glyphs/gallery/five-prime-sticky-restriction-site.png new file mode 100644 index 000000000..178080674 Binary files /dev/null and b/content/visual-glyphs/gallery/five-prime-sticky-restriction-site.png differ diff --git a/content/visual-glyphs/gallery/five-prime-sticky-restriction-site.svg b/content/visual-glyphs/gallery/five-prime-sticky-restriction-site.svg new file mode 100644 index 000000000..36bdcedd3 --- /dev/null +++ b/content/visual-glyphs/gallery/five-prime-sticky-restriction-site.svg @@ -0,0 +1,56 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/generic-sbgn.png b/content/visual-glyphs/gallery/generic-sbgn.png new file mode 100644 index 000000000..887ee627f Binary files /dev/null and b/content/visual-glyphs/gallery/generic-sbgn.png differ diff --git a/content/visual-glyphs/gallery/generic-sbgn.svg b/content/visual-glyphs/gallery/generic-sbgn.svg new file mode 100644 index 000000000..9df369ee7 --- /dev/null +++ b/content/visual-glyphs/gallery/generic-sbgn.svg @@ -0,0 +1,61 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/halfround-rectangle.png b/content/visual-glyphs/gallery/halfround-rectangle.png new file mode 100644 index 000000000..079b86709 Binary files /dev/null and b/content/visual-glyphs/gallery/halfround-rectangle.png differ diff --git a/content/visual-glyphs/gallery/halfround-rectangle.svg b/content/visual-glyphs/gallery/halfround-rectangle.svg new file mode 100644 index 000000000..b85ee29af --- /dev/null +++ b/content/visual-glyphs/gallery/halfround-rectangle.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/inert-dna-spacer.png b/content/visual-glyphs/gallery/inert-dna-spacer.png new file mode 100644 index 000000000..86497831e Binary files /dev/null and b/content/visual-glyphs/gallery/inert-dna-spacer.png differ diff --git a/content/visual-glyphs/gallery/inert-dna-spacer.svg b/content/visual-glyphs/gallery/inert-dna-spacer.svg new file mode 100644 index 000000000..938d693bc --- /dev/null +++ b/content/visual-glyphs/gallery/inert-dna-spacer.svg @@ -0,0 +1,16 @@ + + + + + + + + + \ No newline at end of file diff --git a/content/visual-glyphs/gallery/inhibition.png b/content/visual-glyphs/gallery/inhibition.png new file mode 100644 index 000000000..965474997 Binary files /dev/null and b/content/visual-glyphs/gallery/inhibition.png differ diff --git a/content/visual-glyphs/gallery/inhibition.svg b/content/visual-glyphs/gallery/inhibition.svg new file mode 100644 index 000000000..42a7586ea --- /dev/null +++ b/content/visual-glyphs/gallery/inhibition.svg @@ -0,0 +1,63 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/insulator.png b/content/visual-glyphs/gallery/insulator.png new file mode 100644 index 000000000..be7c50803 Binary files /dev/null and b/content/visual-glyphs/gallery/insulator.png differ diff --git a/content/visual-glyphs/gallery/insulator.svg b/content/visual-glyphs/gallery/insulator.svg new file mode 100644 index 000000000..300f963d5 --- /dev/null +++ b/content/visual-glyphs/gallery/insulator.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/intron.png b/content/visual-glyphs/gallery/intron.png new file mode 100644 index 000000000..67b078470 Binary files /dev/null and b/content/visual-glyphs/gallery/intron.png differ diff --git a/content/visual-glyphs/gallery/intron.svg b/content/visual-glyphs/gallery/intron.svg new file mode 100644 index 000000000..345121c32 --- /dev/null +++ b/content/visual-glyphs/gallery/intron.svg @@ -0,0 +1,110 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/location-dna-no-top.png b/content/visual-glyphs/gallery/location-dna-no-top.png new file mode 100644 index 000000000..57ba93e00 Binary files /dev/null and b/content/visual-glyphs/gallery/location-dna-no-top.png differ diff --git a/content/visual-glyphs/gallery/location-dna-no-top.svg b/content/visual-glyphs/gallery/location-dna-no-top.svg new file mode 100644 index 000000000..fc351a942 --- /dev/null +++ b/content/visual-glyphs/gallery/location-dna-no-top.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/location-dna.png b/content/visual-glyphs/gallery/location-dna.png new file mode 100644 index 000000000..390c140bf Binary files /dev/null and b/content/visual-glyphs/gallery/location-dna.png differ diff --git a/content/visual-glyphs/gallery/location-dna.svg b/content/visual-glyphs/gallery/location-dna.svg new file mode 100644 index 000000000..d666ebcad --- /dev/null +++ b/content/visual-glyphs/gallery/location-dna.svg @@ -0,0 +1,64 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/location-protein-no-top.png b/content/visual-glyphs/gallery/location-protein-no-top.png new file mode 100644 index 000000000..eb9e804ff Binary files /dev/null and b/content/visual-glyphs/gallery/location-protein-no-top.png differ diff --git a/content/visual-glyphs/gallery/location-protein-no-top.svg b/content/visual-glyphs/gallery/location-protein-no-top.svg new file mode 100644 index 000000000..f8b994f15 --- /dev/null +++ b/content/visual-glyphs/gallery/location-protein-no-top.svg @@ -0,0 +1,67 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/location-protein.png b/content/visual-glyphs/gallery/location-protein.png new file mode 100644 index 000000000..ae32b406c Binary files /dev/null and b/content/visual-glyphs/gallery/location-protein.png differ diff --git a/content/visual-glyphs/gallery/location-protein.svg b/content/visual-glyphs/gallery/location-protein.svg new file mode 100644 index 000000000..047e6011c --- /dev/null +++ b/content/visual-glyphs/gallery/location-protein.svg @@ -0,0 +1,67 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/location-rna-no-top.png b/content/visual-glyphs/gallery/location-rna-no-top.png new file mode 100644 index 000000000..ab9ab6620 Binary files /dev/null and b/content/visual-glyphs/gallery/location-rna-no-top.png differ diff --git a/content/visual-glyphs/gallery/location-rna-no-top.svg b/content/visual-glyphs/gallery/location-rna-no-top.svg new file mode 100644 index 000000000..ec03a2079 --- /dev/null +++ b/content/visual-glyphs/gallery/location-rna-no-top.svg @@ -0,0 +1,75 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/location-rna.png b/content/visual-glyphs/gallery/location-rna.png new file mode 100644 index 000000000..6e7f49c35 Binary files /dev/null and b/content/visual-glyphs/gallery/location-rna.png differ diff --git a/content/visual-glyphs/gallery/location-rna.svg b/content/visual-glyphs/gallery/location-rna.svg new file mode 100644 index 000000000..540140732 --- /dev/null +++ b/content/visual-glyphs/gallery/location-rna.svg @@ -0,0 +1,70 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/macromolecule.png b/content/visual-glyphs/gallery/macromolecule.png new file mode 100644 index 000000000..0c1a492f2 Binary files /dev/null and b/content/visual-glyphs/gallery/macromolecule.png differ diff --git a/content/visual-glyphs/gallery/macromolecule.svg b/content/visual-glyphs/gallery/macromolecule.svg new file mode 100644 index 000000000..a4f59a9ef --- /dev/null +++ b/content/visual-glyphs/gallery/macromolecule.svg @@ -0,0 +1,9 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/na-sbgn.png b/content/visual-glyphs/gallery/na-sbgn.png new file mode 100644 index 000000000..079b86709 Binary files /dev/null and b/content/visual-glyphs/gallery/na-sbgn.png differ diff --git a/content/visual-glyphs/gallery/na-sbgn.svg b/content/visual-glyphs/gallery/na-sbgn.svg new file mode 100644 index 000000000..ba61ef996 --- /dev/null +++ b/content/visual-glyphs/gallery/na-sbgn.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/ncrna.png b/content/visual-glyphs/gallery/ncrna.png new file mode 100644 index 000000000..a7bd969b6 Binary files /dev/null and b/content/visual-glyphs/gallery/ncrna.png differ diff --git a/content/visual-glyphs/gallery/ncrna.svg b/content/visual-glyphs/gallery/ncrna.svg new file mode 100644 index 000000000..424c993f5 --- /dev/null +++ b/content/visual-glyphs/gallery/ncrna.svg @@ -0,0 +1,68 @@ + + + + + + image/svg+xml + + + + + + + + + + Layer 1 + + + diff --git a/content/visual-glyphs/gallery/no-glyph-assigned.png b/content/visual-glyphs/gallery/no-glyph-assigned.png new file mode 100644 index 000000000..853d305b3 Binary files /dev/null and b/content/visual-glyphs/gallery/no-glyph-assigned.png differ diff --git a/content/visual-glyphs/gallery/no-glyph-assigned.svg b/content/visual-glyphs/gallery/no-glyph-assigned.svg new file mode 100644 index 000000000..c9663a5ba --- /dev/null +++ b/content/visual-glyphs/gallery/no-glyph-assigned.svg @@ -0,0 +1,83 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + [ ] + + diff --git a/content/visual-glyphs/gallery/nuclease-site.png b/content/visual-glyphs/gallery/nuclease-site.png new file mode 100644 index 000000000..915977dc0 Binary files /dev/null and b/content/visual-glyphs/gallery/nuclease-site.png differ diff --git a/content/visual-glyphs/gallery/nuclease-site.svg b/content/visual-glyphs/gallery/nuclease-site.svg new file mode 100644 index 000000000..d85a12364 --- /dev/null +++ b/content/visual-glyphs/gallery/nuclease-site.svg @@ -0,0 +1,64 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/omitted-detail.png b/content/visual-glyphs/gallery/omitted-detail.png new file mode 100644 index 000000000..621a828d5 Binary files /dev/null and b/content/visual-glyphs/gallery/omitted-detail.png differ diff --git a/content/visual-glyphs/gallery/omitted-detail.svg b/content/visual-glyphs/gallery/omitted-detail.svg new file mode 100644 index 000000000..b75c0ae23 --- /dev/null +++ b/content/visual-glyphs/gallery/omitted-detail.svg @@ -0,0 +1,83 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + ... + + diff --git a/content/visual-glyphs/gallery/operator.png b/content/visual-glyphs/gallery/operator.png new file mode 100644 index 000000000..7823ce94b Binary files /dev/null and b/content/visual-glyphs/gallery/operator.png differ diff --git a/content/visual-glyphs/gallery/operator.svg b/content/visual-glyphs/gallery/operator.svg new file mode 100644 index 000000000..0ce83bc11 --- /dev/null +++ b/content/visual-glyphs/gallery/operator.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/origin-of-replication.png b/content/visual-glyphs/gallery/origin-of-replication.png new file mode 100644 index 000000000..ae3043282 Binary files /dev/null and b/content/visual-glyphs/gallery/origin-of-replication.png differ diff --git a/content/visual-glyphs/gallery/origin-of-replication.svg b/content/visual-glyphs/gallery/origin-of-replication.svg new file mode 100644 index 000000000..024c1bec7 --- /dev/null +++ b/content/visual-glyphs/gallery/origin-of-replication.svg @@ -0,0 +1,57 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/origin-of-transfer.png b/content/visual-glyphs/gallery/origin-of-transfer.png new file mode 100644 index 000000000..61421a2f8 Binary files /dev/null and b/content/visual-glyphs/gallery/origin-of-transfer.png differ diff --git a/content/visual-glyphs/gallery/origin-of-transfer.svg b/content/visual-glyphs/gallery/origin-of-transfer.svg new file mode 100644 index 000000000..12ce558ca --- /dev/null +++ b/content/visual-glyphs/gallery/origin-of-transfer.svg @@ -0,0 +1,130 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/polyA.png b/content/visual-glyphs/gallery/polyA.png new file mode 100644 index 000000000..0f9044930 Binary files /dev/null and b/content/visual-glyphs/gallery/polyA.png differ diff --git a/content/visual-glyphs/gallery/polyA.svg b/content/visual-glyphs/gallery/polyA.svg new file mode 100644 index 000000000..70c59808f --- /dev/null +++ b/content/visual-glyphs/gallery/polyA.svg @@ -0,0 +1,66 @@ + +image/svg+xmlAAA + \ No newline at end of file diff --git a/content/visual-glyphs/gallery/polypeptide-region.png b/content/visual-glyphs/gallery/polypeptide-region.png new file mode 100644 index 000000000..10bcc0042 Binary files /dev/null and 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a/content/visual-glyphs/gallery/process-specification.png b/content/visual-glyphs/gallery/process-specification.png new file mode 100644 index 000000000..968babbf5 Binary files /dev/null and b/content/visual-glyphs/gallery/process-specification.png differ diff --git a/content/visual-glyphs/gallery/process-specification.svg b/content/visual-glyphs/gallery/process-specification.svg new file mode 100644 index 000000000..0fa167aee --- /dev/null +++ b/content/visual-glyphs/gallery/process-specification.svg @@ -0,0 +1,76 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/process.png b/content/visual-glyphs/gallery/process.png new file mode 100644 index 000000000..886b96dcc Binary files /dev/null and b/content/visual-glyphs/gallery/process.png differ diff --git a/content/visual-glyphs/gallery/process.svg b/content/visual-glyphs/gallery/process.svg new file mode 100644 index 000000000..4425273c1 --- /dev/null +++ b/content/visual-glyphs/gallery/process.svg @@ -0,0 +1,62 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/promoter.png b/content/visual-glyphs/gallery/promoter.png new file mode 100644 index 000000000..7ea4efc0f Binary files /dev/null and b/content/visual-glyphs/gallery/promoter.png differ diff --git a/content/visual-glyphs/gallery/promoter.svg b/content/visual-glyphs/gallery/promoter.svg new file mode 100644 index 000000000..e496628d9 --- /dev/null +++ b/content/visual-glyphs/gallery/promoter.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/protease-site.png b/content/visual-glyphs/gallery/protease-site.png new file mode 100644 index 000000000..906b81ba0 Binary files /dev/null and b/content/visual-glyphs/gallery/protease-site.png differ diff --git a/content/visual-glyphs/gallery/protease-site.svg b/content/visual-glyphs/gallery/protease-site.svg new file mode 100644 index 000000000..36551f568 --- /dev/null +++ b/content/visual-glyphs/gallery/protease-site.svg @@ -0,0 +1,104 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/protein-stability-element.png b/content/visual-glyphs/gallery/protein-stability-element.png new file mode 100644 index 000000000..065a5ec9c Binary files /dev/null and b/content/visual-glyphs/gallery/protein-stability-element.png differ diff --git a/content/visual-glyphs/gallery/protein-stability-element.svg b/content/visual-glyphs/gallery/protein-stability-element.svg new file mode 100644 index 000000000..8df399bed --- /dev/null +++ b/content/visual-glyphs/gallery/protein-stability-element.svg @@ -0,0 +1,76 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/protein.png b/content/visual-glyphs/gallery/protein.png new file mode 100644 index 000000000..1c841d46b Binary files /dev/null and b/content/visual-glyphs/gallery/protein.png differ diff --git a/content/visual-glyphs/gallery/protein.svg b/content/visual-glyphs/gallery/protein.svg new file mode 100644 index 000000000..80d1a8779 --- /dev/null +++ b/content/visual-glyphs/gallery/protein.svg @@ -0,0 +1,62 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/replacement-glyph.png b/content/visual-glyphs/gallery/replacement-glyph.png new file mode 100644 index 000000000..3d8ca5941 Binary files /dev/null and b/content/visual-glyphs/gallery/replacement-glyph.png differ diff --git a/content/visual-glyphs/gallery/replacement-glyph.svg b/content/visual-glyphs/gallery/replacement-glyph.svg new file mode 100644 index 000000000..8c33d5714 --- /dev/null +++ b/content/visual-glyphs/gallery/replacement-glyph.svg @@ -0,0 +1,74 @@ + +image/svg+xml? + \ No newline at end of file diff --git a/content/visual-glyphs/gallery/ribonuclease-site.png b/content/visual-glyphs/gallery/ribonuclease-site.png new file mode 100644 index 000000000..61825a964 Binary files 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a/content/visual-glyphs/gallery/rna-stability-element.png b/content/visual-glyphs/gallery/rna-stability-element.png new file mode 100644 index 000000000..0f9c130fe Binary files /dev/null and b/content/visual-glyphs/gallery/rna-stability-element.png differ diff --git a/content/visual-glyphs/gallery/rna-stability-element.svg b/content/visual-glyphs/gallery/rna-stability-element.svg new file mode 100644 index 000000000..b463d0bcb --- /dev/null +++ b/content/visual-glyphs/gallery/rna-stability-element.svg @@ -0,0 +1,86 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/signature.png b/content/visual-glyphs/gallery/signature.png new file mode 100644 index 000000000..60d5bb9a1 Binary files /dev/null and b/content/visual-glyphs/gallery/signature.png differ diff --git a/content/visual-glyphs/gallery/signature.svg b/content/visual-glyphs/gallery/signature.svg new file mode 100644 index 000000000..4a3a3f1bd --- /dev/null +++ b/content/visual-glyphs/gallery/signature.svg @@ -0,0 +1,68 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/simple-chemical-circle.png b/content/visual-glyphs/gallery/simple-chemical-circle.png new file mode 100644 index 000000000..b059033b8 Binary files /dev/null and b/content/visual-glyphs/gallery/simple-chemical-circle.png differ diff --git a/content/visual-glyphs/gallery/simple-chemical-circle.svg b/content/visual-glyphs/gallery/simple-chemical-circle.svg new file mode 100644 index 000000000..c2d3197b8 --- /dev/null +++ b/content/visual-glyphs/gallery/simple-chemical-circle.svg @@ -0,0 +1,66 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/simple-chemical-hexagon.png b/content/visual-glyphs/gallery/simple-chemical-hexagon.png new file mode 100644 index 000000000..793cff431 Binary files /dev/null and b/content/visual-glyphs/gallery/simple-chemical-hexagon.png differ diff --git a/content/visual-glyphs/gallery/simple-chemical-hexagon.svg b/content/visual-glyphs/gallery/simple-chemical-hexagon.svg new file mode 100644 index 000000000..dd369d1e6 --- /dev/null +++ b/content/visual-glyphs/gallery/simple-chemical-hexagon.svg @@ -0,0 +1,70 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/simple-chemical-pentagon.png b/content/visual-glyphs/gallery/simple-chemical-pentagon.png new file mode 100644 index 000000000..a5bf278cc Binary files /dev/null and b/content/visual-glyphs/gallery/simple-chemical-pentagon.png differ diff --git a/content/visual-glyphs/gallery/simple-chemical-pentagon.svg b/content/visual-glyphs/gallery/simple-chemical-pentagon.svg new file mode 100644 index 000000000..f424e51ce --- /dev/null +++ b/content/visual-glyphs/gallery/simple-chemical-pentagon.svg @@ -0,0 +1,70 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/simple-chemical-triangle.png b/content/visual-glyphs/gallery/simple-chemical-triangle.png new file mode 100644 index 000000000..a9a63eea5 Binary files /dev/null and b/content/visual-glyphs/gallery/simple-chemical-triangle.png differ diff --git a/content/visual-glyphs/gallery/simple-chemical-triangle.svg b/content/visual-glyphs/gallery/simple-chemical-triangle.svg new file mode 100644 index 000000000..5c264d416 --- /dev/null +++ b/content/visual-glyphs/gallery/simple-chemical-triangle.svg @@ -0,0 +1,71 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/specific-recombination-site.png b/content/visual-glyphs/gallery/specific-recombination-site.png new file mode 100644 index 000000000..038f2e4bb Binary files /dev/null and b/content/visual-glyphs/gallery/specific-recombination-site.png differ diff --git a/content/visual-glyphs/gallery/specific-recombination-site.svg b/content/visual-glyphs/gallery/specific-recombination-site.svg new file mode 100644 index 000000000..6b59879ad --- /dev/null +++ b/content/visual-glyphs/gallery/specific-recombination-site.svg @@ -0,0 +1,59 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/ssNA.png b/content/visual-glyphs/gallery/ssNA.png new file mode 100644 index 000000000..937f09e0f Binary files /dev/null and b/content/visual-glyphs/gallery/ssNA.png differ diff --git a/content/visual-glyphs/gallery/ssNA.svg b/content/visual-glyphs/gallery/ssNA.svg new file mode 100644 index 000000000..aef5dff36 --- /dev/null +++ b/content/visual-glyphs/gallery/ssNA.svg @@ -0,0 +1,66 @@ + + + + + + image/svg+xml + + + + + + + + + + Layer 1 + + + diff --git a/content/visual-glyphs/gallery/stimulation.png b/content/visual-glyphs/gallery/stimulation.png new file mode 100644 index 000000000..a792447da Binary files /dev/null and b/content/visual-glyphs/gallery/stimulation.png differ diff --git a/content/visual-glyphs/gallery/stimulation.svg b/content/visual-glyphs/gallery/stimulation.svg new file mode 100644 index 000000000..bbcbc915b --- /dev/null +++ b/content/visual-glyphs/gallery/stimulation.svg @@ -0,0 +1,75 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/terminator.png b/content/visual-glyphs/gallery/terminator.png new file mode 100644 index 000000000..fc26c68c1 Binary files /dev/null and b/content/visual-glyphs/gallery/terminator.png differ diff --git a/content/visual-glyphs/gallery/terminator.svg b/content/visual-glyphs/gallery/terminator.svg new file mode 100644 index 000000000..7c64ab174 --- /dev/null +++ b/content/visual-glyphs/gallery/terminator.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/three-prime-overhang.png b/content/visual-glyphs/gallery/three-prime-overhang.png new file mode 100644 index 000000000..bc2bebb03 Binary files /dev/null and b/content/visual-glyphs/gallery/three-prime-overhang.png differ diff --git a/content/visual-glyphs/gallery/three-prime-overhang.svg b/content/visual-glyphs/gallery/three-prime-overhang.svg new file mode 100644 index 000000000..ce966d40a --- /dev/null +++ b/content/visual-glyphs/gallery/three-prime-overhang.svg @@ -0,0 +1,60 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/three-prime-sticky-restriction-site.png b/content/visual-glyphs/gallery/three-prime-sticky-restriction-site.png new file mode 100644 index 000000000..527db15fa Binary files /dev/null and b/content/visual-glyphs/gallery/three-prime-sticky-restriction-site.png differ diff --git a/content/visual-glyphs/gallery/three-prime-sticky-restriction-site.svg b/content/visual-glyphs/gallery/three-prime-sticky-restriction-site.svg new file mode 100644 index 000000000..ee9bd1831 --- /dev/null +++ b/content/visual-glyphs/gallery/three-prime-sticky-restriction-site.svg @@ -0,0 +1,56 @@ + +image/svg+xml \ No newline at end of file diff --git a/content/visual-glyphs/gallery/transcription-end.png b/content/visual-glyphs/gallery/transcription-end.png new file mode 100644 index 000000000..826f5635f Binary files /dev/null and b/content/visual-glyphs/gallery/transcription-end.png differ diff --git a/content/visual-glyphs/gallery/transcription-end.svg b/content/visual-glyphs/gallery/transcription-end.svg new file mode 100644 index 000000000..89e65403c --- /dev/null +++ b/content/visual-glyphs/gallery/transcription-end.svg @@ -0,0 +1,75 @@ + +image/svg+xml* + \ No newline at end of file diff --git a/content/visual-glyphs/gallery/translation-end.png b/content/visual-glyphs/gallery/translation-end.png new file mode 100644 index 000000000..b05b93a60 Binary files /dev/null and b/content/visual-glyphs/gallery/translation-end.png differ diff --git a/content/visual-glyphs/gallery/translation-end.svg b/content/visual-glyphs/gallery/translation-end.svg new file mode 100644 index 000000000..edcba243e --- /dev/null +++ b/content/visual-glyphs/gallery/translation-end.svg @@ -0,0 +1,81 @@ + +image/svg+xml* + \ No newline at end of file diff --git a/content/visual-glyphs/gallery/unspecified-glyph.png b/content/visual-glyphs/gallery/unspecified-glyph.png new file mode 100644 index 000000000..3d8ca5941 Binary files /dev/null and b/content/visual-glyphs/gallery/unspecified-glyph.png differ diff --git a/content/visual-glyphs/gallery/unspecified-glyph.svg b/content/visual-glyphs/gallery/unspecified-glyph.svg new file mode 100644 index 000000000..8c33d5714 --- /dev/null +++ b/content/visual-glyphs/gallery/unspecified-glyph.svg @@ -0,0 +1,74 @@ + +image/svg+xml? + \ No newline at end of file diff --git a/content/visual-glyphs/index.md b/content/visual-glyphs/index.md new file mode 100644 index 000000000..fd2c42bd8 --- /dev/null +++ b/content/visual-glyphs/index.md @@ -0,0 +1,16 @@ +--- +title: SBOL Visual Glyphs +type: visual-glyphs +layout: single +--- + +SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}). +These glyphs are made to be drawable on a white board but they are not definite, they are guidelines. +Sample visual glyphs are supported in PDF, PNG, SVG. +Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual. +Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs. +Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. + +Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. + +Zip files containing all glyphs as PDF, PNG, or SVG can be downloaded from the [Releases page](https://github.com/SynBioDex/SBOL-visual/releases) of the SBOL Visual GitHub repository. diff --git a/data/fonts/nacelle.toml b/data/fonts/nacelle.toml new file mode 100644 index 000000000..59f5f2727 --- /dev/null +++ b/data/fonts/nacelle.toml @@ -0,0 +1,3 @@ +# Minimal font definition for Wowchemy +heading = "Nacelle" +body = "Nacelle" \ No newline at end of file diff --git a/data/glyphs.yaml b/data/glyphs.yaml new file mode 100644 index 000000000..206c846b8 --- /dev/null +++ b/data/glyphs.yaml @@ -0,0 +1,149 @@ +groups: + - name: "Sequence Features" + glyphs: + - file: "aptamer.svg" + name: "Aptamer" + - file: "assembly-scar.svg" + name: "Assembly Scar" + - file: "blunt-restriction-site.svg" + name: "Blunt Restriction Site" + - file: "cds.svg" + name: "CDS" + - file: "cds-arrow.svg" + name: "CDS" + - file: "chromosomal-locus.svg" + name: "Chromosomal Locus" + - file: "circular-plasmid.svg" + name: "Circular Plasmid" + - file: "nuclease-site.svg" + name: "Cleavage Site" + - file: "protease-site.svg" + name: "Cleavage Site" + - file: "ribonuclease-site.svg" + name: "Cleavage Site" + - file: "composite.svg" + name: "Composite" + - file: "engineered-region.svg" + name: "Engineered Region" + - file: "inert-dna-spacer.svg" + name: "Inert DNA Spacer" + - file: "intron.svg" + name: "Intron" + - file: "location-dna-no-top.svg" + name: "Location" + - file: "location-dna.svg" + name: "Location" + - file: "location-protein-no-top.svg" + name: "Location" + - file: "location-protein.svg" + name: "Location" + - file: "location-rna-no-top.svg" + name: "Location" + - file: "location-rna.svg" + name: "Location" + - file: "no-glyph-assigned.svg" + name: "No Glyph Assigned" + - file: "ncrna.svg" + name: "Non-Coding RNA" + - file: "omitted-detail.svg" + name: "Omitted Detail" + - file: "operator.svg" + name: "Operator" + - file: "origin-of-replication.svg" + name: "Origin of Replication" + - file: "origin-of-transfer.svg" + name: "Origin of Transfer" + - file: "five-prime-overhang.svg" + name: "Overhang" + - file: "three-prime-overhang.svg" + name: "Overhang" + - file: "polyA.svg" + name: "PolyA Site" + - file: "polypeptide-region.svg" + name: "Polypeptide Region" + - file: "primer-binding-site.svg" + name: "Primer Binding Site" + - file: "promoter.svg" + name: "Promoter" + - file: "ribosome-entry-site.svg" + name: "Ribosome Entry Site" + - file: "signature.svg" + name: "Signature" + - file: "specific-recombination-site.svg" + name: "Specific Recombination Site" + - file: "dna-stability-element.svg" + name: "Stability Element" + - file: "rna-stability-element.svg" + name: "Stability Element" + - file: "protein-stability-element.svg" + name: "Stability Element" + - file: "five-prime-sticky-restriction-site.svg" + name: "Sticky Restriction Site" + - file: "three-prime-sticky-restriction-site.svg" + name: "Sticky Restriction Site" + - file: "transcription-end.svg" + name: "Stop Site" + - file: "translation-end.svg" + name: "Stop Site" + - file: "terminator.svg" + name: "Terminator" + - file: "halfround-rectangle.svg" + name: "Unspecified" + - file: "unspecified-glyph.svg" + name: "Unspecified" + + - name: "Molecular Species" + glyphs: + - file: "complex-sbgn.svg" + name: "Complex" + - file: "dsNA.svg" + name: "Double-Stranded Nucleic Acid" + - file: "na-sbgn.svg" + name: "Double-Stranded Nucleic Acid" + - file: "macromolecule.svg" + name: "Macromolecule" + - file: "no-glyph-assigned.svg" + name: "No Glyph Assigned" + - file: "protein.svg" + name: "Protein" + - file: "simple-chemical-circle.svg" + name: "Simple Chemical" + - file: "simple-chemical-hexagon.svg" + name: "Simple Chemical" + - file: "simple-chemical-pentagon.svg" + name: "Simple Chemical" + - file: "simple-chemical-triangle.svg" + name: "Simple Chemical" + - file: "ssNA.svg" + name: "Single-Stranded Nucleic Acid" + - file: "na-sbgn.svg" + name: "Single-Stranded Nucleic Acid" + - file: "generic-sbgn.svg" + name: "Unspecified" + - file: "replacement-glyph.svg" + name: "Unspecified" + + - name: "Interactions" + glyphs: + - file: "control.svg" + name: "Control" + - file: "degradation.svg" + name: "Degradation" + - file: "inhibition.svg" + name: "Inhibition" + - file: "process-specification.svg" + name: "Process" + - file: "stimulation.svg" + name: "Stimulation" + + - name: "Interaction Nodes" + glyphs: + - file: "association.svg" + name: "Association" + - file: "dissociation.svg" + name: "Dissociation" + - file: "process.svg" + name: "Process" + - file: "replacement-glyph.svg" + name: "Unspecified" + diff --git a/docs/editors/01-announcements.md b/docs/editors/01-announcements.md new file mode 100644 index 000000000..1edf3e93d --- /dev/null +++ b/docs/editors/01-announcements.md @@ -0,0 +1,85 @@ +# Adding an Announcement + +Announcements appear in the **News → Announcements** section of the site and on the homepage feed. Use them for event notices, new releases, calls for abstracts, and other time-sensitive community news. + +--- + +## Where the files live + +``` +content/post/ +└── your-announcement-slug/ + └── index.md +``` + +Each announcement is a folder inside `content/post/`. The folder name becomes part of the URL (e.g. `content/post/combine-2026/` → `sbolstandard.org/post/combine-2026/`). Keep it short, lowercase, and hyphenated. + +--- + +## Step-by-step + +1. Create a new folder inside `content/post/` with a short descriptive name. +2. Inside that folder, create a file called `index.md`. +3. Copy the front matter template below and fill in the fields. +4. Write the body of the announcement in plain Markdown below the closing `---`. + +--- + +## Template + +```markdown +--- +title: "Your Announcement Title" +date: 2026-06-01 +summary: > + One or two sentences that appear in the card preview on the homepage + and listings page. Keep it under 200 characters. +tags: + - Events # add relevant tags; common ones: Events, Release, Community +--- + +Write the full announcement here in plain Markdown. + +You can use headings, bullet lists, tables, bold text, and links. +``` + +--- + +## Real example + +`content/post/combine-2026/index.md` + +```markdown +--- +title: "COMBINE 2026 — Workshop at Keele University, UK" +date: 2026-05-09 +summary: > + The 2026 COMBINE Workshop will be held at Keele University, UK, from + 7–10 September 2026. Registration and abstract submission are now open. +tags: + - Events + - COMBINE + - Community +--- + +The **Computational Modeling in Biology Network (COMBINE)** ... +``` + +--- + +## Field reference + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Shown as the heading on the post page and in cards | +| `date` | Yes | ISO format (`YYYY-MM-DD`). Used for ordering — most recent appears first | +| `summary` | Yes | Short preview text shown in cards and the homepage feed | +| `tags` | No | Freeform list. Common values: `Events`, `Release`, `Community`, `COMBINE`, `HARMONY` | + +--- + +## Common mistakes + +- **Wrong folder** — files must be inside `content/post/`, not `content/blog/`. Blog posts and announcements are separate sections. +- **Missing `index.md`** — the file must be named exactly `index.md` (lowercase). +- **Date in the future** — Hugo will still publish it, but double-check the date is what you intend. diff --git a/docs/editors/02-blog-post.md b/docs/editors/02-blog-post.md new file mode 100644 index 000000000..335c882f1 --- /dev/null +++ b/docs/editors/02-blog-post.md @@ -0,0 +1,100 @@ +# Adding a Blog Post + +Blog posts appear in the **News → Blog** section. Use them for longer-form content: tutorials, perspectives, tool spotlights, or community stories. Unlike announcements, blog posts are not primarily time-sensitive — they are evergreen articles. + +--- + +## Where the files live + +``` +content/blog/ +└── your-post-slug/ + ├── index.md + └── featured.png ← optional cover image +``` + +--- + +## Step-by-step + +1. Create a new folder inside `content/blog/` with a short descriptive name (lowercase, hyphenated). +2. Inside that folder, create `index.md`. +3. Optionally add a cover image named `featured.png` or `featured.jpg` in the same folder. +4. Fill in the front matter and write the post body in Markdown. + +--- + +## Template + +```markdown +--- +title: "Your Post Title" +date: 2026-06-01 +authors: + - your-author-slug # must match a folder name under content/authors/ +tags: + - SBOL + - Tutorial +summary: "One or two sentences describing the post. Shown in the card preview." +featured: false +image: + caption: "" + focal_point: "Smart" +--- + +Write your post here in plain Markdown. +``` + +--- + +## Real example + +`content/blog/sample-post/index.md` + +```markdown +--- +title: "Welcome to the SBOL Blog" +date: 2026-05-17 +authors: + - prashant-vaidyanathan +tags: + - synthetic biology + - SBOL + - community +summary: "Introducing the new SBOL community blog..." +featured: false +image: + caption: "" + focal_point: "" +--- + +Welcome to the SBOL community blog... +``` + +--- + +## Field reference + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Heading shown on the post page and in cards | +| `date` | Yes | ISO format (`YYYY-MM-DD`) | +| `authors` | No | List of author slugs from `content/authors/`. Leave blank to omit author attribution | +| `tags` | No | Freeform list used for filtering | +| `summary` | Yes | Short preview shown in card listings | +| `featured` | No | Set to `true` to pin as the lead article at the top of the blog page | +| `image.focal_point` | No | Where to crop the cover image. Options: `Smart`, `Center`, `Top`, `Bottom`, `Left`, `Right` | + +--- + +## Author slugs + +Author slugs are the folder names under `content/authors/`. For example, `prashant-vaidyanathan` corresponds to `content/authors/prashant-vaidyanathan/`. If you are a new author, see the [Leadership guide](07-leadership.md) for how to create an author profile — the same profile is used for blog attribution. + +--- + +## Common mistakes + +- **Wrong folder** — blog posts go in `content/blog/`, not `content/post/`. Posts in `content/post/` appear as announcements. +- **Author slug not found** — if the slug doesn't match an existing folder under `content/authors/`, the author line is silently dropped. Check the folder name carefully. +- **Cover image wrong name** — the image must be named `featured.png` or `featured.jpg` exactly. Any other name will be ignored. diff --git a/docs/editors/03-library.md b/docs/editors/03-library.md new file mode 100644 index 000000000..1f088ee7c --- /dev/null +++ b/docs/editors/03-library.md @@ -0,0 +1,122 @@ +# Adding a Library + +Libraries appear on the **Ecosystem → Libraries** page, organised into SBOL 2 and SBOL 3 tabs. Each library has a category that controls where it appears within a tab. + +--- + +## Where the files live + +``` +content/libraries/ +└── your-library-slug/ + ├── index.md + └── featured.png ← logo or screenshot (recommended) +``` + +--- + +## Step-by-step + +1. Create a new folder inside `content/libraries/` (lowercase, hyphenated). +2. Add `index.md` with the front matter below. +3. Optionally add `featured.png` — a logo or screenshot shown on the card. +4. Write a description of the library in Markdown below the closing `---`. + +--- + +## Template + +```markdown +--- +title: "Library Name" +summary: "One sentence describing what the library does." +tags: + - Libraries +sbol_versions: ["3"] # "2", "3", or ["2", "3"] for both +lib_category: library # see categories below +date: "2026-06-01T00:00:00Z" + +external_link: "" + +image: + focal_point: Smart + +links: + - icon: github + icon_pack: fab + name: GitHub + url: https://github.com/your-org/your-repo + - icon: edge + icon_pack: fab + name: Documentation + url: https://your-docs-url.com +--- + +Write a description of the library here. Explain what it does, what language it targets, and any relevant background. +``` + +--- + +## Real example + +`content/libraries/sbol3-py/index.md` + +```markdown +--- +title: Python +summary: Python interfaces and implementations for SBOL +tags: + - Libraries +sbol_versions: ["3"] +lib_category: primary +date: "2022-02-15T16:30:18Z" +external_link: "" +image: + focal_point: Smart +links: + - icon: github + icon_pack: fab + name: Github + url: https://github.com/SynBioDex/pySBOL3 + - icon: edge + icon_pack: fab + name: API & Documentation + url: https://pysbol3.readthedocs.io +--- + +[pySBOL3](https://opensource.org/licenses/MIT) provides Python interfaces... +``` + +--- + +## Field reference + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Displayed as the library name | +| `summary` | Yes | One-line description shown in the card | +| `sbol_versions` | Yes | Controls which tab the library appears in. Use `["2"]`, `["3"]`, or `["2","3"]` | +| `lib_category` | Yes | Controls the section within the tab (see below) | +| `date` | Yes | ISO 8601 format. Used for ordering within a section | +| `links` | No | List of icon buttons shown on the card. See icon packs below | +| `external_link` | No | If set, the card title links here instead of to the detail page | + +### `lib_category` values + +| Value | Where it appears | +|---|---| +| `primary` | "Primary Libraries" — actively maintained core implementations | +| `library` | "Libraries" — community-contributed implementations | +| `resource` | "Resources" — notebooks, utilities, and other tooling | + +### Link icon packs + +Icons come from Font Awesome. Use `icon_pack: fab` for brand icons (GitHub, npm) and `icon_pack: fas` for solid icons (tools, bug, code). Browse available icons at [fontawesome.com](https://fontawesome.com/icons). + +--- + +## Common mistakes + +- **Wrong `sbol_versions` format** — must be a YAML list: `["3"]` not just `3`. +- **Unknown `lib_category`** — only the three values above are recognised; typos cause the entry to be silently omitted. +- **Image not named `featured`** — the card image must be `featured.png` or `featured.jpg`. diff --git a/docs/editors/04-application.md b/docs/editors/04-application.md new file mode 100644 index 000000000..e405e8861 --- /dev/null +++ b/docs/editors/04-application.md @@ -0,0 +1,113 @@ +# Adding an Application + +Applications appear on the **Ecosystem → Applications** page. These are tools, platforms, and software that use or support SBOL — distinct from libraries (which are code packages developers import into their own projects). + +--- + +## Where the files live + +``` +content/applications/ +└── your-app-slug/ + ├── index.md + └── featured.png ← screenshot or logo (recommended) +``` + +--- + +## Step-by-step + +1. Create a new folder inside `content/applications/` (lowercase, hyphenated). +2. Add `index.md` with the front matter below. +3. Add `featured.png` — a screenshot or logo is strongly recommended as it appears on the card. +4. Write a description in Markdown below the closing `---`. + +--- + +## Template + +```markdown +--- +title: "Your Application Name" +summary: "One sentence describing what the tool does." +tags: + - Design # see common tags below +date: "2026-06-01T00:00:00Z" +active: true # set to false to move to the Deprecated section + +external_link: "" + +image: + focal_point: Smart + +links: + - icon: edge + icon_pack: fab + name: Website + url: https://your-tool-url.com + - icon: github + icon_pack: fab + name: GitHub + url: https://github.com/your-org/your-repo +--- + +Write a description of the application here. +``` + +--- + +## Real example + +`content/applications/synbiohub/index.md` + +```markdown +--- +title: SynBioHub +summary: A registry for storing and sharing genetic circuit designs using the SBOL2 standard +tags: + - Repository + - Visualization +date: "2020-06-30T00:00:00Z" +external_link: "" +image: + focal_point: Smart +links: + - icon: edge + icon_pack: fab + name: Link + url: https://synbiohub.org/ + - icon: github + icon_pack: fab + name: GitHub + url: https://github.com/SynBioDex/SynBioHub +--- + +SynBioHub is a repository for sharing genetic designs... +``` + +--- + +## Field reference + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Name of the application | +| `summary` | Yes | One-line description shown in the card | +| `tags` | Yes | Used by the filter bar on the Applications page. See common tags below | +| `date` | Yes | ISO 8601 format. Used for ordering | +| `active` | No | Defaults to `true`. Set to `false` to move to the Deprecated section at the bottom of the page | +| `external_link` | No | If set, clicking the card goes directly here instead of a detail page | + +### Common tags + +`Design`, `Repository`, `Visualization`, `Simulation`, `Conversion`, `Validation`, `Education`, `Notebook` + +You can introduce new tags — they will automatically appear in the filter bar. Keep them concise (one or two words). + +--- + +## Common mistakes + +- **No `featured.png`** — applications without an image display a blank card, which looks unfinished. Add a screenshot or logo. +- **Too many tags** — two or three tags per application is enough. More dilutes the filter bar. +- **Using `active: false` instead of deleting** — prefer `active: false` for deprecated tools so the history is preserved on the site. diff --git a/docs/editors/05-genai-tool.md b/docs/editors/05-genai-tool.md new file mode 100644 index 000000000..35459b24a --- /dev/null +++ b/docs/editors/05-genai-tool.md @@ -0,0 +1,74 @@ +# Adding a GenAI Tool + +GenAI tools appear on the **Ecosystem → GenAI Tools** page. These are AI-powered assistants, models, or resources that help users understand or work with SBOL — for example, custom GPTs trained on the specification. + +--- + +## Where the files live + +``` +content/genai-tools/ +└── your-tool-slug/ + └── index.md +``` + +No image is needed — the cards are text-based. + +--- + +## Step-by-step + +1. Create a new folder inside `content/genai-tools/` (lowercase, hyphenated). +2. Add `index.md` with the front matter below. +3. That's it — no other files needed. + +--- + +## Template + +```markdown +--- +title: "Your Tool Name" +summary: "Two or three sentences describing what the tool does and who it is for." +external_url: "https://link-to-the-tool.com" +platform: "ChatGPT" # the platform the tool runs on, e.g. ChatGPT, HuggingFace +sbol_version: "3" # "2", "3", or omit if not version-specific +--- +``` + +> **Important:** Use `external_url`, not `url`. Hugo reserves `url` as the page's own address — using it here will cause a build error. + +--- + +## Real example + +`content/genai-tools/sbol3-gpt/index.md` + +```markdown +--- +title: "SBOL 3 GPT" +summary: "A custom ChatGPT assistant trained on the SBOL 3 specification and the pySBOL3 library. Ask it anything about SBOL 3 data models, syntax, and Python usage." +external_url: "https://chatgpt.com/g/g-FcRCPqKq6-sbol-3" +platform: "ChatGPT" +sbol_version: "3" +--- +``` + +--- + +## Field reference + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Name of the tool, shown as the card heading | +| `summary` | Yes | Description shown on the card. Two or three sentences works well | +| `external_url` | Yes | The link users click to open the tool. Must be `external_url`, not `url` | +| `platform` | No | Shown as a badge on the card (e.g. `ChatGPT`, `HuggingFace`, `Notebook`) | +| `sbol_version` | No | Shown as a green `SBOL 2` or `SBOL 3` badge. Omit if not version-specific | + +--- + +## Common mistakes + +- **Using `url` instead of `external_url`** — Hugo treats `url` as the page's own path. If you use an `https://` URL there, the build will fail with an error about unsupported URL protocols. +- **Leaving `platform` blank** — the platform badge helps users quickly understand what environment the tool runs in. Always fill it in if you know it. diff --git a/docs/editors/06-visual-gallery.md b/docs/editors/06-visual-gallery.md new file mode 100644 index 000000000..95a734124 --- /dev/null +++ b/docs/editors/06-visual-gallery.md @@ -0,0 +1,137 @@ +# Adding an Image to the Visual Gallery + +The Visual Gallery (`/visual-gallery/`) showcases SBOL Visual diagrams from published manuscripts. Each image has its own folder containing the image file, a short `index.md`, and optionally a `cite.bib` file for automatic citation parsing. + +--- + +## Where the files live + +``` +content/visual-gallery/ +└── your-image-slug/ + ├── index.md + ├── image.png ← the diagram (also .jpg, .jpeg, .gif, .webp, .svg) + └── cite.bib ← optional but recommended +``` + +The folder name becomes the URL slug — use a short identifier from the paper (e.g. the DOI suffix or first author + year). + +--- + +## Step-by-step + +### With a BibTeX file (recommended) + +1. Create a new folder inside `content/visual-gallery/`. +2. Add the diagram image (any common image format). +3. Add `cite.bib` with the BibTeX entry for the paper. +4. Add `index.md` with just the title, DOI, and publication URL — everything else is read from the `.bib` file automatically. + +### Without a BibTeX file + +Provide all fields directly in the `index.md` front matter instead. + +--- + +## Template (with cite.bib — recommended) + +**`index.md`** +```markdown +--- +title: "Full title of the paper this image is from" +doi: "10.1021/acssynbio.1c00281" +publication_url: "https://pubs.acs.org/doi/10.1021/acssynbio.1c00281" +--- +``` + +**`cite.bib`** +```bibtex +@article{yourkeyhere, + title={Full paper title}, + author={Last, First and Second, Author}, + journal={Journal Name}, + volume={10}, + number={12}, + pages={3330--3342}, + year={2021}, + publisher={Publisher Name} +} +``` + +The site automatically extracts `author`, `year`, `journal`, and `doi` from the `.bib` file. The `doi` in `index.md` takes priority over the `.bib` if both are present. + +--- + +## Template (without cite.bib) + +```markdown +--- +title: "Full title of the paper" +credit: "Last Name, First Name and Second Author" +year: 2021 +publication: "ACS Synthetic Biology" +doi: "10.1021/acssynbio.1c00281" +publication_url: "https://pubs.acs.org/doi/10.1021/acssynbio.1c00281" +--- + +Optional caption describing what the diagram shows. +``` + +--- + +## Real example + +`content/visual-gallery/sb1c00281/` + +``` +sb1c00281/ +├── index.md +├── image.jpeg +└── cite.bib +``` + +`index.md`: +```markdown +--- +title: "Predicting composition of genetic circuits with resource competition: demand and sensitivity" +doi: "10.1021/acssynbio.1c00281" +publication_url: "https://pubs.acs.org/doi/10.1021/acssynbio.1c00281" +--- +``` + +`cite.bib`: +```bibtex +@article{mcbride2021predicting, + title={Predicting composition of genetic circuits with resource competition: demand and sensitivity}, + author={McBride, Cameron D and Del Vecchio, Domitilla}, + journal={ACS Synthetic Biology}, + volume={10}, + number={12}, + pages={3330--3342}, + year={2021}, + publisher={ACS Publications} +} +``` + +--- + +## Field reference (index.md) + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Full paper title. Shown in the card and lightbox | +| `doi` | Recommended | DOI string only, without `https://doi.org/`. Shown as a link in the lightbox | +| `publication_url` | Recommended | Full URL to the paper. Used for the "View Publication" button | +| `credit` | No | Override for author attribution if not using `cite.bib` | +| `year` | No | Override for year if not using `cite.bib` | +| `publication` | No | Override for journal name if not using `cite.bib` | + +The body of `index.md` (below the closing `---`) is used as a caption in the lightbox. + +--- + +## Common mistakes + +- **Image not found** — the image must be in the same folder as `index.md`. The gallery picks up the first image file it finds (`*.jpg`, `*.jpeg`, `*.png`, `*.gif`, `*.webp`, `*.svg`). +- **`.bib` file not parsed** — the parser reads the `.bib` file line by line. Make sure each field (`author`, `year`, `journal`, `doi`) is on its own line in standard BibTeX format. +- **`authors` as a field name** — do not use `authors` in the front matter. Wowchemy reserves that field and expects a list; using it as a string causes a build error. Use `credit` instead. diff --git a/docs/editors/07-leadership.md b/docs/editors/07-leadership.md new file mode 100644 index 000000000..f973f7daf --- /dev/null +++ b/docs/editors/07-leadership.md @@ -0,0 +1,122 @@ +# Adding or Editing a Person on the Leadership Page + +The Leadership page (`/community-leadership/`) is powered by Wowchemy's people widget. Each person has a profile folder under `content/authors/`. The same profiles are used for blog post attribution. + +--- + +## Where the files live + +``` +content/authors/ +└── firstname-lastname/ + ├── _index.md + └── avatar.jpg ← headshot photo +``` + +The folder name is the person's slug (used in blog `authors:` lists and internal links). Use lowercase with hyphens. + +--- + +## Step-by-step + +### Adding a new person + +1. Create a new folder inside `content/authors/` (e.g. `content/authors/jane-smith/`). +2. Add `_index.md` with the front matter below. +3. Add a headshot photo named `avatar.jpg` or `avatar.png` in the same folder. + +### Editing an existing person + +Open the relevant `content/authors//_index.md` and update the fields directly. + +### Changing someone's group (e.g. moving a chair to Past Chairs) + +Update the `user_groups` list in their `_index.md`. A person can belong to multiple groups and will appear in each section on the Leadership page. + +--- + +## Template + +```markdown +--- +title: Jane Smith +role: "SBOL Editor (2024–present)" +weight: 10 # lower numbers appear first within a section +organizations: + - name: University of Example + url: "https://example.ac.uk" +social: + - icon: envelope + icon_pack: fas + link: mailto:jane@example.ac.uk + - icon: github + icon_pack: fab + link: https://github.com/janesmithgithub + - icon: linkedin + icon_pack: fab + link: https://linkedin.com/in/janesmith +user_groups: + - Current Editors +--- + +Optional short bio in plain Markdown. Appears on the person's profile page. +``` + +--- + +## Real example + +`content/authors/prashant-vaidyanathan/_index.md` + +```markdown +--- +title: Prashant Vaidyanathan +role: "SBOL Chair (2023–present)" +weight: 10 +organizations: + - name: Oxford Biomedica + url: "" +user_groups: + - Current Chair + - Past Editors +--- +``` + +--- + +## Field reference + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Full name as it should appear on the site | +| `role` | No | Job title or SBOL role. For Past Chairs, include tenure dates (e.g. `SBOL Chair (2019–2022)`) | +| `weight` | No | Controls ordering within a section. Lower = appears earlier. Default is unordered | +| `organizations` | No | List of `name` + `url` pairs. `url` can be empty | +| `social` | No | List of social/contact links with Font Awesome icons | +| `user_groups` | Yes | Controls which section(s) on the Leadership page the person appears in | + +### Valid `user_groups` values + +| Value | Section on Leadership page | +|---|---| +| `Current Chair` | Current Chair | +| `Current Editors` | Current Editors | +| `Steering Committee` | Steering Committee | +| `Advisory Board` | Advisory Board | +| `Past Chairs` | Past Chairs | +| `Past Editors` | Past Editors | + +A person can be in multiple groups (e.g. someone who is both a Steering Committee member and a Past Editor). + +### `role` visibility + +The `role` field is shown only in the **Past Chairs** section. In all other sections it is hidden, so the section heading itself provides the context. For Past Chairs, use the tenure format: `SBOL Chair (2019–2022)`. + +--- + +## Common mistakes + +- **File named `index.md` not `_index.md`** — author profiles must use `_index.md` (with the leading underscore). A file named `index.md` will not be picked up as an author profile. +- **Wrong `user_groups` value** — the value must match exactly (including capitalisation). A typo means the person does not appear on the Leadership page. +- **Avatar not found** — without `avatar.jpg` or `avatar.png`, a grey placeholder is shown. Add a headshot whenever possible. +- **`authors` vs `credit`** — when listing someone as a blog post author, use their slug in the post's `authors:` list, not their full name. diff --git a/docs/editors/08-publication.md b/docs/editors/08-publication.md new file mode 100644 index 000000000..f907089de --- /dev/null +++ b/docs/editors/08-publication.md @@ -0,0 +1,136 @@ +# Adding a Publication + +Publications appear on the **Publications** page (`/publication/`). Each publication has its own folder containing a BibTeX file and an `index.md`. + +--- + +## Where the files live + +``` +content/publication/ +└── firstauthor-shorttitle-year/ + ├── index.md + └── cite.bib +``` + +Use a descriptive slug for the folder name — the convention in this repo is `firstauthor-keyword-year` (e.g. `mcbride-resource-competition-2021`). Keep it lowercase and hyphenated. + +--- + +## Step-by-step + +1. Create a new folder inside `content/publication/`. +2. Add `cite.bib` with the BibTeX entry. +3. Add `index.md` with the front matter below. + +--- + +## Template + +**`cite.bib`** +```bibtex +@article{yourkeyhere, + title={Full paper title}, + author={Last, First and Second, Author}, + journal={Journal Name}, + volume={10}, + number={4}, + pages={1234--1250}, + year={2026}, + publisher={Publisher Name}, + doi={10.xxxx/xxxxxxx} +} +``` + +**`index.md`** +```markdown +--- +title: "Full paper title" +date: "2026-06-01T00:00:00Z" +authors: + - First Last + - Second Author +publication: "*Journal Name*, vol. 10, no. 4" +publication_types: + - "2" # see publication types below +abstract: "Paste the abstract here." +featured: false +url_pdf: "" # direct link to PDF if openly available +doi: "10.xxxx/xxxxxxx" +--- +``` + +--- + +## Real example + +`content/publication/appleton-interactive-2014/` + +`cite.bib`: +```bibtex +@article{appleton2014interactive, + title={Interactive assembly algorithms for molecular cloning}, + author={Appleton, Evan and Tao, Jenhan and Haddock, Traci and Densmore, Douglas}, + journal={Nature Methods}, + volume={11}, + number={6}, + pages={657--662}, + year={2014}, + publisher={Nature Publishing Group} +} +``` + +`index.md`: +```markdown +--- +title: "Interactive assembly algorithms for molecular cloning" +date: "2014-06-01T00:00:00Z" +authors: + - Evan Appleton + - Jenhan Tao + - Traci Haddock + - Douglas Densmore +publication: "*Nature Methods*, vol. 11, no. 6" +publication_types: + - "2" +abstract: "" +featured: false +doi: "" +--- +``` + +--- + +## Field reference + +| Field | Required | Notes | +|---|---|---| +| `title` | Yes | Full paper title | +| `date` | Yes | Publication date in ISO 8601 format | +| `authors` | Yes | List of author full names as plain strings | +| `publication` | Yes | Journal name in italics using `*asterisks*`, plus volume/issue if known | +| `publication_types` | Yes | List with a single type code (see below) | +| `abstract` | No | Paper abstract. Can be left blank | +| `featured` | No | Set to `true` to feature the paper prominently | +| `url_pdf` | No | Direct link to a PDF. Leave blank if not openly available | +| `doi` | No | DOI string only, without `https://doi.org/` | + +### Publication type codes + +| Code | Meaning | +|---|---| +| `"1"` | Conference paper | +| `"2"` | Journal article | +| `"3"` | Preprint | +| `"4"` | Report | +| `"5"` | Book | +| `"6"` | Book chapter | +| `"7"` | Thesis | + +--- + +## Common mistakes + +- **Missing `cite.bib`** — both files are required. The BibTeX file is used by the "Cite" button on the publication page. +- **Authors as slugs** — unlike blog posts, publication `authors` are plain name strings, not slugs from `content/authors/`. Write the full name as it should appear. +- **Wrong date format** — use the full ISO 8601 format including time: `"2026-06-01T00:00:00Z"`. diff --git a/layouts/applications/list.html b/layouts/applications/list.html new file mode 100644 index 000000000..8678c5146 --- /dev/null +++ b/layouts/applications/list.html @@ -0,0 +1,157 @@ +{{ define "main" }} + +{{/* ── Collect pages ── */}} +{{ $active := where .Pages "Params.active" "!=" false }} +{{ $deprecated := where .Pages "Params.active" false }} + +{{/* ── Unique tag set from all pages ── */}} +{{ $tags := slice }} +{{ range .Pages }} +{{ range .Params.tags }} +{{ $tags = $tags | append . }} +{{ end }} +{{ end }} +{{ $tags = $tags | uniq | sort }} + +{{/* ── Submit URL from section front matter ── */}} +{{ $submitURL := .Params.submit_url | default "" }} + +{{/* ── Hero ── */}} +
+
+ +

{{ .Title }}

+

{{ .Params.subtitle }}

+
+
+ +
+ + {{/* ── Filter bar ── */}} +
+ + {{ range $tags }} + {{ $t := . }} + {{ $count := 0 }} + {{ range $active }} + {{ if in .Params.tags $t }}{{ $count = add $count 1 }}{{ end }} + {{ end }} + + {{ end }} +
+ + {{/* ── Card grid ── */}} +
+ + {{ range $active }} + {{ $url := "" }} + {{ with .Params.links }}{{ $url = (index . 0).url }}{{ end }} + {{ if not $url }}{{ $url = .Params.external_link }}{{ end }} + +
+
+ {{ .Title }} + {{ with $url }} + + + + + + + + {{ end }} +
+

{{ .Summary | plainify | truncate 130 "…" }}

+
+ {{ range .Params.tags }} + {{ . }} + {{ end }} +
+
+ {{ end }} + + {{/* ── Submit a Tool CTA card ── */}} + {{ with $submitURL }} +
+
+ + + + + +
+

Submit a Tool

+

Built something that supports SBOL? Let the community know.

+ Submit +
+ {{ end }} + +
{{/* /app-grid */}} + + {{/* ── Deprecated section ── */}} + {{ with $deprecated }} +
+

Legacy Tools

+

Preserved here for reference - these tools supported SBOL at the time of listing. +

+ +
+ {{ range . }} + {{ $url := "" }} + {{ with .Params.links }}{{ $url = (index . 0).url }}{{ end }} + {{ if not $url }}{{ $url = .Params.external_link }}{{ end }} +
+ + {{ .Title }} + + Legacy +

{{ .Summary | plainify | truncate 100 "…" }}

+
+ {{ range .Params.tags }} + {{ . }} + {{ end }} +
+
+ {{ end }} +
+
+ {{ end }} + +
{{/* /universal-wrapper */}} + + + +{{ end }} \ No newline at end of file diff --git a/layouts/biologist/list.html b/layouts/biologist/list.html new file mode 100644 index 000000000..6a537dc1a --- /dev/null +++ b/layouts/biologist/list.html @@ -0,0 +1,240 @@ +{{ define "main" }} + +{{ $p := .Params }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ $p.subtitle }}

+
+
+ +
+ + {{/* ── Benefits ── */}} + {{ with $p.benefits }} +
+ {{ range . }} +
+
+

{{ .title }}

+

{{ .description }}

+
+ {{ end }} +
+ {{ end }} + + {{/* ── Tools ── */}} + {{ range $p.tools }} + {{ $img := $.Resources.GetMatch .image }} +
+
+ {{ with $img }} + + {{ end }} +
+
+

{{ .name }}

+

{{ .description }}

+
    + {{ range .bullets }}
  • {{ . }}
    • {{ end }} +
+ {{ .cta_text }} +
+
+ {{ end }} + +
{{/* /universal-wrapper */}} + +{{/* ── Visual Language ── */}} +{{ with $p.glyphs_title }} +
+
+

{{ . }}

+

{{ $p.glyphs_description }}

+
+ {{ with $p.glyphs_url }} + + + Browse the Glyphs + Full glyph library + + {{ end }} + {{ with $p.glyphs_gallery_url }} + + + View the Gallery + Diagrams from published papers + + {{ end }} + {{ with $p.glyphs_history_url }} + + + 10 Years of SBOL Visual + How the standard evolved + + {{ end }} +
+
+
+{{ end }} + +{{/* ── GenAI tools ── */}} +{{ with $p.genai_title }} +
+
+
+
+

{{ . }}

+

{{ $p.genai_description }}

+
+ {{ with $p.genai_url }} + Explore AI Tools + {{ end }} +
+
+{{ end }} + + + +{{ end }} diff --git a/layouts/blog/list.html b/layouts/blog/list.html new file mode 100644 index 000000000..3a12f2030 --- /dev/null +++ b/layouts/blog/list.html @@ -0,0 +1,66 @@ +{{ define "main" }} + +{{/* ── Hero header ── */}} +
+
+

SBOL Blog

+

Insights, tutorials, and perspectives from the synthetic biology community.

+
+
+ +
+ + {{ $pages := .Pages }} + {{ $top := first 1 $pages }} + {{ $rest := after 1 $pages }} + + {{/* ── Featured / lead post ── */}} + {{ range $top }} + {{ $resource := (.Resources.ByType "image").GetMatch "*featured*" }} + + {{ if $resource }} + {{ $img := $resource.Fill "900x520 Smart" }} +
+ {{ .Title }} +
+ {{ end }} +
+ {{ with .Params.tags }} +
{{ range first 3 . }}{{ . }}{{ end }}
+ {{ end }} +

{{ .Title }}

+

{{ .Date.Format "January 2, 2006" }}

+ {{ with .Params.summary }}

{{ . }}

{{ end }} + Read article → +
+ + {{ end }} + + {{/* ── Card grid ── */}} + {{ if $rest }} +
+ {{ range $rest }} + {{ $resource := (.Resources.ByType "image").GetMatch "*featured*" }} + + {{ if $resource }} + {{ $img := $resource.Fill "600x360 Smart" }} +
+ {{ .Title }} +
+ {{ end }} +
+ {{ with .Params.tags }} +
{{ range first 2 . }}{{ . }}{{ end }}
+ {{ end }} +

{{ .Title }}

+

{{ .Date.Format "Jan 2, 2006" }}

+ {{ with .Params.summary }}

{{ . | plainify | truncate 130 "…" }}

{{ end }} + Read more → +
+ + {{ end }} +
+ {{ end }} + +
+{{ end }} diff --git a/layouts/community-meetings/list.html b/layouts/community-meetings/list.html new file mode 100644 index 000000000..a51090f02 --- /dev/null +++ b/layouts/community-meetings/list.html @@ -0,0 +1,427 @@ +{{ define "main" }} + +{{ $now := now }} +{{ $meetings := .Params.meetings | default slice }} +{{ $outreach := .Params.outreach | default slice }} +{{ $connectLinks := .Params.connect_links | default slice }} +{{ $connectText := .Params.connect_text | default "" }} +{{ $heroBtnText := .Params.hero_btn_text | default "Join the Community" }} +{{ $heroBtnIcon := .Params.hero_btn_icon | default "" }} +{{ $heroBtnUrl := .Params.hero_btn_url | default "" }} + +{{/* ── Split meetings: upcoming vs archive ── */}} +{{ $upcoming := slice }} +{{ $past := slice }} +{{ range $meetings }} + {{ $d := "" }} + {{ with .date }}{{ $d = time . }}{{ end }} + {{ if and $d (ge $d $now) }} + {{ $upcoming = $upcoming | append . }} + {{ else }} + {{ $past = $past | append . }} + {{ end }} +{{ end }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ .Params.subtitle }}

+ {{ with $heroBtnUrl }} + + {{ with $heroBtnIcon }}{{ end }}{{ $heroBtnText }} + + {{ end }} +
+
+ +
+ + {{/* ── Workshops & Conferences ── */}} +
+

Workshops & Conferences

+ +
+ + +
+ +
+ {{ if $upcoming }} + + + + {{ range $upcoming }} + + + + + + + {{ end }} + +
EventDateLocationResources
+ {{ .type }} + {{ if .url }}{{ .name }} + {{ else }}{{ .name }}{{ end }} + {{ .date_display }}{{ .location }}{{ with .slides_url }}Slides{{ end }}
+ {{ else }} +

No upcoming events scheduled — check back soon.

+ {{ end }} +
+ +
+ {{ if $past }} + + + + {{ range $past }} + + + + + + + {{ end }} + +
EventDateLocationResources
+ {{ .type }} + {{ if .url }}{{ .name }} + {{ else }}{{ .name }}{{ end }} + {{ .date_display }}{{ .location }}{{ with .slides_url }}Slides{{ end }}
+ {{ end }} +
+
+ + {{/* ── Outreach & Education ── */}} + {{ $outreachUpcoming := slice }} + {{ $outreachPast := slice }} + {{ range $outreach }} + {{ $d := "" }} + {{ with .date }}{{ $d = time . }}{{ end }} + {{ if and $d (ge $d $now) }} + {{ $outreachUpcoming = $outreachUpcoming | append . }} + {{ else }} + {{ $outreachPast = $outreachPast | append . }} + {{ end }} + {{ end }} + +
+

Outreach & Education

+ +
+ + +
+ +
+ {{ if $outreachUpcoming }} +
+ {{ range $outreachUpcoming }} +
+ {{ .type }} + {{ if .url }} + {{ .name }} + {{ else }} + {{ .name }} + {{ end }} + {{ .date_display }}{{ with .location }} · {{ . }}{{ end }} +
+ {{ end }} +
+ {{ else }} +

No upcoming outreach events scheduled — check back soon.

+ {{ end }} +
+ +
+ {{ if $outreachPast }} +
+ {{ range $outreachPast }} +
+ {{ .type }} + {{ if .url }} + {{ .name }} + {{ else }} + {{ .name }} + {{ end }} + {{ .date_display }}{{ with .location }} · {{ . }}{{ end }} +
+ {{ end }} +
+ {{ end }} +
+
+ +
{{/* /universal-wrapper */}} + +{{/* ── Stay Connected ── */}} +{{ if $connectLinks }} +
+
+

Stay Connected

+ {{ with $connectText }}

{{ . }}

{{ end }} +
+ {{ range $connectLinks }} + + {{ with .icon }} {{ end }}{{ .name }} + {{ .description }} + + {{ end }} +
+
+
+{{ end }} + + + + + +{{ end }} diff --git a/layouts/developer/list.html b/layouts/developer/list.html new file mode 100644 index 000000000..1d2a75cce --- /dev/null +++ b/layouts/developer/list.html @@ -0,0 +1,231 @@ +{{ define "main" }} + +{{ $p := .Params }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ $p.subtitle }}

+
+
+ +
+ + {{/* ── Benefits ── */}} + {{ with $p.benefits }} +
+ {{ range . }} +
+
+

{{ .title }}

+

{{ .description }}

+
+ {{ end }} +
+ {{ end }} + + {{/* ── Libraries ── */}} + {{ with $p.libraries_title }} +
+
+

{{ . }}

+

{{ $p.libraries_description }}

+ Browse All Libraries +
+
+ {{ end }} + + {{/* ── Specification ── */}} + {{ with $p.spec_title }} +
+

{{ . }}

+

{{ $p.spec_description }}

+
+ {{ range $p.spec_links }} + + + {{ .label }} + {{ .description }} + + {{ end }} +
+
+ {{ end }} + + {{/* ── Toolchain ── */}} + {{ with $p.toolchain_title }} +
+

{{ . }}

+

{{ $p.toolchain_description }}

+
+ {{ range $p.toolchain_links }} + + + {{ .label }} + {{ .description }} + + {{ end }} +
+
+ {{ end }} + +
{{/* /universal-wrapper */}} + +{{/* ── GenAI ── */}} +{{ with $p.genai_title }} +
+
+
+
+

{{ . }}

+

{{ $p.genai_description }}

+
+ {{ with $p.genai_url }} + Explore AI Tools + {{ end }} +
+
+{{ end }} + +{{/* ── Contribute ── */}} +{{ with $p.contribute_title }} +
+
+

{{ . }}

+

{{ $p.contribute_description }}

+
+ {{ range $p.contribute_links }} + + + {{ .label }} + {{ .description }} + + {{ end }} +
+
+
+{{ end }} + + + +{{ end }} diff --git a/layouts/genai-tools/list.html b/layouts/genai-tools/list.html new file mode 100644 index 000000000..79cb426cc --- /dev/null +++ b/layouts/genai-tools/list.html @@ -0,0 +1,118 @@ +{{ define "main" }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ .Params.subtitle }}

+
+
+ +
+
+ {{ range .Pages }} + {{ $url := .Params.external_url | default .Permalink }} + {{ $platform := .Params.platform | default "" }} + {{ $version := .Params.sbol_version | default "" }} + +
+ {{ with $platform }} + {{ . }} + {{ end }} + {{ with $version }} + SBOL {{ . }} + {{ end }} +
+

{{ .Title }}

+

{{ .Params.summary }}

+ Try it → + + {{ end }} +
+
+ + + +{{ end }} diff --git a/layouts/join/list.html b/layouts/join/list.html new file mode 100644 index 000000000..42086e8c3 --- /dev/null +++ b/layouts/join/list.html @@ -0,0 +1,266 @@ +{{ define "main" }} + +{{ $p := .Params }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ $p.subtitle }}

+
+
+ +
+ + {{/* ── Reasons ── */}} + {{ with $p.reasons }} +
+ {{ range . }} +
+
+

{{ .title }}

+

{{ .description }}

+
+ {{ end }} +
+ {{ end }} + + {{/* ── Stats ── */}} + {{ with $p.stats }} +
+
+ {{ range . }} +
+ {{ .number }} + {{ .label }} +
+ {{ end }} +
+ {{ with $p.stats_note }} +

{{ . }}

+ {{ end }} +
+ {{ end }} + + {{/* ── Connect ── */}} + {{ with $p.connect_title }} +
+

{{ . }}

+
+ {{ range $p.connect_links }} + + + {{ .label }} + {{ .description }} + + {{ end }} +
+
+ {{ end }} + + {{/* ── Meetings ── */}} + {{ with $p.meetings_title }} +
+
+

{{ . }}

+

{{ $p.meetings_description }}

+ {{ with $p.meetings_url }} + View Meetings & Outreach + {{ end }} +
+
+ {{ end }} + + {{/* ── Structure ── */}} + {{ with $p.structure_title }} +
+

{{ . }}

+

{{ $p.structure_description }}

+
+ {{ range $p.structure_links }} + + + {{ .label }} + {{ .description }} + + {{ end }} +
+
+ {{ end }} + +
{{/* /universal-wrapper */}} + +{{/* ── CTA ── */}} +{{ with $p.cta_title }} +
+
+

{{ . }}

+

{{ $p.cta_description }}

+ {{ with $p.cta_btn_url }} + {{ $p.cta_btn_text }} + {{ end }} +
+
+{{ end }} + + + +{{ end }} diff --git a/layouts/libraries/list.html b/layouts/libraries/list.html new file mode 100644 index 000000000..d1165fda3 --- /dev/null +++ b/layouts/libraries/list.html @@ -0,0 +1,199 @@ +{{ define "main" }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ .Params.subtitle }}

+ +
+
+ +{{/* ── Tab bar ── */}} +
+
+ {{ range $i, $tab := .Params.tabs }} + + {{ end }} +
+
+ +
+ + {{ range $i, $tab := $.Params.tabs }} + {{ $tabID := $tab.id }} + + {{/* Filter pages for this version */}} + {{ $tabPages := slice }} + {{ range $.Pages }} + {{ if in .Params.sbol_versions $tabID }} + {{ $tabPages = $tabPages | append . }} + {{ end }} + {{ end }} + + {{ $primary := where $tabPages "Params.lib_category" "primary" }} + {{ $libraries := where $tabPages "Params.lib_category" "library" }} + {{ $resources := where $tabPages "Params.lib_category" "resource" }} + +
+ + {{/* ── Primary Libraries ── */}} + {{ with $primary }} +
+
+

Primary Libraries

+

Actively maintained core implementations.

+
+ {{ if eq $tabID "3" }}Active Development{{ end }} +
+
+ {{ range . }} + {{ $github := "" }} + {{ $docs := "" }} + {{ range .Params.links }} + {{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }} + {{ if or (in .name "Documentation") (in .name "API") (eq .icon "edge") }}{{ $docs = .url }}{{ end }} + {{ end }} +
+
+ {{ .Title }} + {{ with $github }} + + + + + + + + {{ end }} +
+

{{ .Summary | plainify }}

+
+ {{ with $docs }} + Documentation + {{ end }} + {{ with $github }} + GitHub + {{ end }} + More Info +
+
+ {{ end }} +
+ {{ end }} + + {{/* ── Other Libraries ── */}} + {{ with $libraries }} +
+
+

Other Libraries

+

Additional language implementations.

+
+
+
+ {{ range . }} + {{ $github := "" }} + {{ $docs := "" }} + {{ range .Params.links }} + {{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }} + {{ if or (in .name "Documentation") (in .name "API") (eq .icon "edge") }}{{ $docs = .url }}{{ end }} + {{ end }} +
+
+ {{ .Title }} + {{ with $github }} + + + + + + + + {{ end }} +
+

{{ .Summary | plainify }}

+
+ {{ with $docs }} + Documentation + {{ end }} + {{ with $github }} + GitHub + {{ end }} + More Info +
+
+ {{ end }} +
+ {{ end }} + + {{/* ── Developer Resources ── */}} + {{ with $resources }} +
+
+
+

Developer Resources

+

Tools and notebooks to accelerate your work with SBOL.

+
+
+
+ {{ range . }} + {{ $github := "" }} + {{ range .Params.links }} + {{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }} + {{ end }} +
+

{{ .Title }}

+

{{ .Summary | plainify }}

+ {{ with $github }} + Explore on GitHub → + {{ end }} +
+ {{ end }} +
+
+ {{ end }} + +
{{/* /lib-panel */}} + {{ end }}{{/* /range tabs */}} + +
{{/* /universal-wrapper */}} + + + +{{ end }} \ No newline at end of file diff --git a/layouts/partials/site_footer.html b/layouts/partials/site_footer.html new file mode 100644 index 000000000..1e2aea19b --- /dev/null +++ b/layouts/partials/site_footer.html @@ -0,0 +1,12 @@ +
+ {{ if site.Menus.footer }} +

+ {{ range site.Menus.footer }} + {{ .Name }} + {{ end }} +

+ {{ end }} +

© 2026 SBOL. This webpage is under license CC BY NC ND + 4.0

+
\ No newline at end of file diff --git a/layouts/shortcodes/card.html b/layouts/shortcodes/card.html new file mode 100644 index 000000000..1a4f2b2a6 --- /dev/null +++ b/layouts/shortcodes/card.html @@ -0,0 +1,10 @@ +{{- $title := .Get "title" -}} +{{- $image := .Get "image" -}} +{{- $link := .Get "link" -}} + + +
+ {{ $title }} +
+
{{ $title }}
+ diff --git a/layouts/shortcodes/hero-feed.html b/layouts/shortcodes/hero-feed.html new file mode 100644 index 000000000..40ce9e2a9 --- /dev/null +++ b/layouts/shortcodes/hero-feed.html @@ -0,0 +1,190 @@ +{{- /* + hero-feed: Two-column hero shortcode. + Parameters: + badge — small pill label above the title (optional) + title — H1 headline (required) + subtitle — paragraph below the title (required) + btn1_text — primary button label + btn1_link — primary button URL + btn2_text — secondary button label + btn2_link — secondary button URL + + Note: Contains an embedded + +
+ + {{/* ── Left column ── */}} +
+ {{ with $badge }}{{ . }}{{ end }} +

{{ $title }}

+

{{ $subtitle }}

+
+ {{ with $btn1_text }} + {{ . }} + {{ end }} + {{ with $btn2_text }} + {{ with $btn2_icon }}{{ end }}{{ . }} + {{ end }} +
+
+ + {{/* ── Right column — recent posts feed ── */}} +
+

What's Happening

+ + {{ $announcements := where site.RegularPages "Section" "post" }} + {{ $blog := where site.RegularPages "Section" "blog" }} + {{ $all := $announcements | append $blog }} + {{ $all = sort $all ".Date" "desc" }} + {{ $recent := first 2 $all }} + + {{ if $recent }} + {{ range $recent }} +
+
+ {{ if eq .Section "blog" }} + Blog + {{ else }} + Announcement + {{ end }} + {{ .Date.Format "Jan 2, 2006" }} +
+
+ {{ .Title }} +
+ {{ with .Summary }} +
{{ . | plainify | truncate 120 "…" }}
+ {{ end }} +
+ {{ end }} + {{ else }} +

No posts yet — check back soon.

+ {{ end }} +
+ +
diff --git a/layouts/shortcodes/journey-cards.html b/layouts/shortcodes/journey-cards.html new file mode 100644 index 000000000..fd08adcca --- /dev/null +++ b/layouts/shortcodes/journey-cards.html @@ -0,0 +1,64 @@ +{{- /* + journey-cards: Responsive 3-column card grid container. + Use with nested {{< card >}} shortcodes. + Embed once per page — the + +
+ {{ .Inner }} +
diff --git a/layouts/sponsor-sbol/list.html b/layouts/sponsor-sbol/list.html new file mode 100644 index 000000000..444462016 --- /dev/null +++ b/layouts/sponsor-sbol/list.html @@ -0,0 +1,337 @@ +{{ define "main" }} + +{{ $benefits := .Params.benefits | default slice }} +{{ $pastSponsors := .Params.past_sponsors | default slice }} +{{ $bdacURL := .Params.bdac_url | default "https://bio-design-automation.org" }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ .Params.subtitle }}

+ + Support via BDAC + +
+
+ +
+ + {{/* ── About SBOL ── */}} +
+

SBOL is open and community-powered

+
+
+ +

An international standard

+

SBOL is the globally recognized data standard for synthetic biology, used by researchers and engineers across academia and industry to share and exchange biological designs.

+
+
+ +

Volunteer-driven

+

The SBOL community is a volunteer organization. There are no membership fees and participation is open to all. The standard remains free and open by design.

+
+
+ +

Staying visible takes effort

+

Keeping SBOL present at conferences, active in publications, and relevant to tool developers requires sustained organizational support from the broader community.

+
+
+
+ + {{/* ── How it works ── */}} +
+

How sponsorship works

+

Sponsorship for SBOL flows through the Bio-Design Automation Consortium (BDAC). BDAC is the umbrella organization for the biodesign automation community, and supporting BDAC is supporting SBOL.

+
+
+
1
+
+

Contact BDAC

+

Reach out to the Bio-Design Automation Consortium to discuss supporting the community.

+
+
+ +
+
2
+
+

Fund the consortium

+

Your contribution supports the BDAC community, including SBOL standards development, tooling, and outreach.

+
+
+ +
+
3
+
+

SBOL recognizes your support

+

BDAC sponsors receive acknowledgment across SBOL's presentations, website, and community communications.

+
+
+
+
+ + {{/* ── Benefits ── */}} + {{ with $benefits }} +
+

What your support means for SBOL

+
+ {{ range . }} +
+
+

{{ .title }}

+

{{ .body }}

+
+ {{ end }} +
+
+ {{ end }} + + {{/* ── Past Sponsors ── */}} + {{ with $pastSponsors }} +
+

Organizations that have supported SBOL

+

These organizations previously supported SBOL through the SBOL Industrial Consortium. We are grateful for their contributions to the community.

+
+ {{ range . }} +
+ {{ .name }} +
+ {{ end }} +
+
+ {{ end }} + +
{{/* /universal-wrapper */}} + +{{/* ── CTA ── */}} +
+
+

Interested in supporting SBOL?

+

Get in touch with BDAC to learn how your organization can help sustain the synthetic biology open language standard.

+ + Visit BDAC   + +
+
+ + + +{{ end }} diff --git a/layouts/visual-gallery/list.html b/layouts/visual-gallery/list.html new file mode 100644 index 000000000..1ebe7a3f4 --- /dev/null +++ b/layouts/visual-gallery/list.html @@ -0,0 +1,296 @@ +{{ define "main" }} + +{{ $submitURL := .Params.submit_url | default "" }} + +{{/* ── Hero ── */}} +
+
+

{{ .Title }}

+

{{ .Params.subtitle }}

+ {{ with $submitURL }} + + Recommend an Image + + {{ end }} +
+
+ +
+ + {{/* ── Image grid ── */}} +
+ {{ range .Pages }} + {{ $page := . }} + {{ $img := .Resources.GetMatch "*.{jpg,jpeg,png,gif,webp,svg}" }} + + {{/* Initialise from front matter */}} + {{ $credit := $page.Params.credit | default "" }} + {{ $year := printf "%v" ($page.Params.year | default "") }} + {{ $journal := $page.Params.publication | default "" }} + {{ $doi := $page.Params.doi | default "" }} + {{ $pubUrl := $page.Params.publication_url | default "" }} + + {{/* + Parse cite.bib using readFile (bypasses Hugo Markdown renderer). + No ^ anchor in patterns: leading whitespace survives Go template trim. + */}} + {{ with $page.File }} + {{ $bibRaw := readFile (printf "content/%scite.bib" .Dir) }} + {{ if $bibRaw }} + {{ range (split $bibRaw "\n") }} + {{ if findRE `(?i)author\s*=\s*\{` . }} + {{ $credit = . | replaceRE `(?i).*author\s*=\s*\{(.+)\}.*` "$1" | replaceRE ` and others$` "" }} + {{ end }} + {{ if findRE `(?i)\byear\s*=\s*\{` . }} + {{ $year = . | replaceRE `(?i).*\byear\s*=\s*\{(\d{4})\}.*` "$1" }} + {{ end }} + {{ if findRE `(?i)\bjournal\s*=\s*\{` . }} + {{ $journal = . | replaceRE `(?i).*\bjournal\s*=\s*\{(.+)\}.*` "$1" }} + {{ end }} + {{ if findRE `(?i)\bdoi\s*=\s*\{` . }} + {{ $doi = . | replaceRE `(?i).*\bdoi\s*=\s*\{(.+)\}.*` "$1" }} + {{ end }} + {{ end }} + {{ if $page.Params.doi }}{{ $doi = $page.Params.doi }}{{ end }} + {{ end }} + {{ end }} + + {{ with $img }} + + {{ end }} + {{ end }} +
+ +
{{/* /universal-wrapper */}} + +{{/* ── Lightbox (native ) ── */}} + +
+ +
+ +
+
+

+

+

+ +
+
+ + + + + + +{{ end }} diff --git a/layouts/visual-glyphs/single.html b/layouts/visual-glyphs/single.html new file mode 100644 index 000000000..303638e69 --- /dev/null +++ b/layouts/visual-glyphs/single.html @@ -0,0 +1,27 @@ +{{ define "main" }} +
+

{{ .Title }}

+
+ {{ .Content }} +
+ + {{ range site.Data.glyphs.groups }} +

{{ .name }}

+
+ {{ $resources := $.Resources.ByType "image" }} + {{ range .glyphs }} + {{ $file := .file }} + {{ $name := .name }} + {{ $img := $resources.GetMatch (printf "gallery/%s" $file) }} + {{ with $img }} + + {{ $name }} + {{ $name }} + + {{ end }} + {{ end }} +
+ {{ end }} + +
+{{ end }} diff --git a/static/fonts/Nacelle-Bold.woff2 b/static/fonts/Nacelle-Bold.woff2 new file mode 100644 index 000000000..7546f5d9f Binary files /dev/null and b/static/fonts/Nacelle-Bold.woff2 differ diff --git a/static/fonts/Nacelle-BoldItalic.woff2 b/static/fonts/Nacelle-BoldItalic.woff2 new file mode 100644 index 000000000..abe49e29a Binary files /dev/null and b/static/fonts/Nacelle-BoldItalic.woff2 differ diff --git a/static/fonts/Nacelle-Heavy.woff2 b/static/fonts/Nacelle-Heavy.woff2 new file mode 100644 index 000000000..265dabe76 Binary files /dev/null and b/static/fonts/Nacelle-Heavy.woff2 differ diff --git a/static/fonts/Nacelle-HeavyItalic.woff2 b/static/fonts/Nacelle-HeavyItalic.woff2 new file mode 100644 index 000000000..ef6415174 Binary files /dev/null and b/static/fonts/Nacelle-HeavyItalic.woff2 differ diff --git a/static/fonts/Nacelle-Italic.woff2 b/static/fonts/Nacelle-Italic.woff2 new file mode 100644 index 000000000..3e6ff2501 Binary files /dev/null and b/static/fonts/Nacelle-Italic.woff2 differ diff --git a/static/fonts/Nacelle-Light.woff2 b/static/fonts/Nacelle-Light.woff2 new file mode 100644 index 000000000..ac63519f1 Binary files /dev/null and b/static/fonts/Nacelle-Light.woff2 differ diff --git a/static/fonts/Nacelle-LightItalic.woff2 b/static/fonts/Nacelle-LightItalic.woff2 new file mode 100644 index 000000000..fb2d0ad29 Binary files /dev/null and b/static/fonts/Nacelle-LightItalic.woff2 differ diff --git a/static/fonts/Nacelle-Regular.woff2 b/static/fonts/Nacelle-Regular.woff2 new file mode 100644 index 000000000..641447152 Binary files /dev/null and b/static/fonts/Nacelle-Regular.woff2 differ diff --git a/static/media/welcome/sbol_biologist.png b/static/media/welcome/sbol_biologist.png new file mode 100644 index 000000000..41088cd05 Binary files /dev/null and b/static/media/welcome/sbol_biologist.png differ diff --git a/static/media/welcome/sbol_developer.png b/static/media/welcome/sbol_developer.png new file mode 100644 index 000000000..1f8f39d1e Binary files /dev/null and b/static/media/welcome/sbol_developer.png differ diff --git a/static/media/welcome/sbol_join.png b/static/media/welcome/sbol_join.png new file mode 100644 index 000000000..6974488ff Binary files /dev/null and b/static/media/welcome/sbol_join.png differ