Question about SSBandDSBWithDBSCAN

[FabioLSBrum]

Simulation question

Hello,

I would like to learn more about the SSBandDSBWithDBSCAN scorer.

From your previous post (#110), I understand that it’s a new scorer that doesn’t require the DBSCAN scorer on its own. Could you clarify the differences between the two? Also, is there a paper describing this method?

I ask because I am trying to score SSB and DSB in TsCircularPlasmid, and I noticed that both methods are mentioned in the TOPAS-nBio/examples/scorers.

Thank you for your time and help.

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Scoring

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[JoseRamosMendez]

Good question.

The difference is the way Topas-nBio passes the spatial information of the energy deposition events to DSBCAN.

1. With the scorer s:Sc/<scorer>/Quantity = "DBSCAN" there is not any DNA geometry. The spatial events are filtered by the energy threshold and a 16% probability (Francis et al) given by u:Sc/<scorer>/ScoreHitsWithProbability=0.16. You could think this probability as a DNA geometry factor to set how "dense" is the DNA in the medium. The position of the "damage" on the DNA helix (left or right) is done with a 50% probability.
2. With the scorer s:Sc/<scorer>/Quantity="SimpleSSBandDSBWithDBSCAN", the spatial events (base pair, strand ID) are filtered by the plasmid/DNA geometries, so you need DNA geometry. In that case, the u:Sc/<scorer>/ScoreHitsWithProbability should be unity although it can still be a free parameter.

In both cases, the classification of SSB and DSB are managed by DBSCAN.

Best!