Software

Software that I developed/maintained/contributed to

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Infrared

A framework for efficient, tree decomposition based solving of declaratively modeled problems. Models can be solved by optimization or Boltzmann sampling.
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VARNA API

A Python package facilitates the usage of VARNA, an RNA secondary structure drawing tool. The package helps to generate command line required to communicate with VARNA.
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VARNAjs

A Javascript library for RNA secondary structure visualization on web.
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RNAPOND

A sampling iterative approach based on Infrared. RNAPOND generates design candidates respecting to positive design objectives while negative design principles are captured by introducing disruptive base pairs at each step.
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BayesPairing2

A tool to identify RNA 3D modules, which is considered as BayesianNetworks, in sequence and alignments.