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@kMutagene kMutagene released this May 30, 2019 · 2 commits to master since this release

0.1.0 - Thursday, May 30, 2019

Several bugfixes and additions to multiple sub projects:

0.0.16 - Thursday, March 7, 2019

  • Fix template files for all nuget packages:
    • use correct paths for binaries
    • update project descriptions
    • use type project to infer dependencies
Assets 2

@kMutagene kMutagene released this Mar 7, 2019 · 39 commits to developer since this 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

Assets 2
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