Model training for Optical DNA mapping

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Dnr:

NAISS 2024/22-957

Type:

NAISS Small Compute

Principal Investigator:

Albertas Dvirnas

Affiliation:

Chalmers tekniska högskola

Start Date:

2024-06-28

End Date:

2025-07-01

Primary Classification:

10203: Bioinformatics (Computational Biology) (applications to be 10610)

Webpage:

https://github.com/dnadevcode/

Allocation

Centre Storage at NSC: 500 GiB
Tetralith at NSC: 10 x 1000 core-h/month

Abstract

We will use the computing resources to train the parameters for the various models in the field of Optical DNA mapping. These include the fitting of the binding constants for the competitive binding model (HCA), parameters for the kymograph alignment (SPALIGN), optimal parameters for local alignment algorithm (MP) and structural variation detection (HMMSV).