Alpha release

This release contains all features we did not track in our release notes (the 0.0.1"Initial release"). For a full overview of BioFSharp's functionality check the documentation.

Additionally, the following features were introduced:

(get nuget packages from the nuget branch)

• ImgP - project introduction:

  • Toolbox for analysis of neuronal calcium-imaging data

• BioFSharp.ML - project introduction:

  • Usage of Microsoft's CNTK library with a biological focus:
  • This project comes with working CNTK integration:
    • necessary dependencies to use CNTK and its unmanaged libraries
    • CNTK loadscript: an easy way to load all dependencies of CNTK. load the script and use the resolveCNTKDependencies() function.
  • Built-in deep neural network 'd::ppop' (publication)
    • predict peptide observability in mass spectrometry
    • Classification: functions to determine peptide feature vectors as input for dppop
    • Prediction: functions to predict peptide observability using the feature vectors prepared in Classification.
    • NonPlant and Plant models as embedded resources: the two models used in the original Web API. Additionally load custom models.

• BioFSharp.BioTools - project introduction:

  • uses docker.dotnet to use docker images and stream their output to fsi
  • Low level wrapping of multiple docker.dotnet functions for F#
  • Basic functionality for using docker images from fsi
  • BioContainer functionality:
    • Add windows/unix path conversions and subpath matching to MounInfo
    • Add execReturnAsync (returns stdout of docker container) and execAsync (redirects stdout/stderr of container)
  • Addition of blast biocontainer support for:
    • BLAST: makeblastdb, blastp, blastn
    • HMMER:
      • hmmbuild
      • hmmalign
      • hmmsearch
      • hmmscan
      • hmmemit
      • hmmpress
      • hmmconvert
    • Hera
    • FastP
    • ClustalO

• Addition of Pretty Printers, SOFT Parser, GEOFTP functions

• Improvement and refactoring of Modification functionality