BioFSharp Versions Save

This pre-release basically only exists to trigger zenodo DOI assignment.

Release notes:

https://github.com/CSBiology/BioFSharp/blob/developer/RELEASE_NOTES.md#200---tbd

Additions:

• BioFSharp.BioDD:
  • Full low-level DSL for generating Entrez queries for NCBI cgis:
    • einfo
    • esearch
    • epost
    • esummary
    • efetch
    • elink
    • egquery
    • espell
    • ecitmatch
• Bugfixes:
  • BioFSharp.BioContainers:
    • fix fastP DSL command line generation (missing = signs)

Additions:

• BioFSharp.BioContainers:
  • Add fasterq-dump and prefetch DSL for the SRATools biocontainer
  • Add full STAR RNASeq aligner DSL for the respective BioContainer. Commit details
• BioFSharp.IO:
  • Add load script for referencing pretty printers, included in the nuget package
  • Add multiple new pretty printers for SOFT

Bugfixes:

• BioFSharp.IO:
  • Fix GFF3 pretty printer return type

1.0.03 - Wednesday, February 26, 2020

• BioFSharp.Stats:
  • Massively improved SAILENT characterization speed for preprocessing of large datasets
• BioFSharp.BioContainers:
  • Improved DSL for Blast biocontainer API
• BioFSharp.IO:
  • Refactored SOFT Parser and improved its namespace encapsulation.
  • add prettyPrinters for the SOFT GSE/GPL type

Combining some minor releases to this large one:

1.0.02 - Wednesday, February 19, 2020

• BioFSharp.BioDB:
  • Fix FaTool OData model URL
• BioFSharp.Vis
  • Add Function to save chord plots as html files

1.0.01 - Thursday, October 24, 2019

• BioFSharp.Stats:
  • Major speed improvements for Sailent

1.0.0 - Wednesday, October 23, 2019

Renaming of BioFSharp.Biotools makes this a major version increase, as it is not backwards compatible. Several bugfixes and additions to multiple sub projects:

• We now have a cool new logo! (See readme)

• BioFSharp.BioTools has been renamed to BioFSharp.BioContainers. This reflects the purpose of the library better than the previous name.

• BioFSharp.BioContainers

  • Add thin LastAlign biocontainer API wrapper

• BioFSharp.IO

  • Bugfixes:
    • Fix SOFT parser skipping entities (fixes #72)

• BioFSharp.Stats

  • Sailent is now faster and has a verbose option (fixes #74,#75)

• BioFSharp.ImgP

  • Add functionality to isolate local maxima from frames
  • Add functionality to get correlation at specified coordinates

0.1.02 - Wednesday, September 04, 2019

Several bugfixes and additions to multiple sub projects:

• BioFSharp (core):

  • Addition of various Unit tests (see the issue to track what has been added since the last version)
  • Bugfixes:
    • Naming clarification and bugfixes regarding reverse and reverse complements for DNA (fixes #66 and #65)

• BioFSharp.Stats

  • Bugfixes
    • Ontology enrichment is now more conservative

0.1.01 - Wednesday, July 31, 2019

Several bugfixes and additions to multiple sub projects:

• BioFSharp (core):

  • Add Unit testing for modules: Formula Mass BioArray
  • Changed functionality:
    • Formula.substract now also returns negative atom counts

• BioFSharp.ML:

  • Additional functionality:
    • add thin CNTK API

0.1.0 - Thursday, May 30, 2019

Several bugfixes and additions to multiple sub projects:

• BioFSharp (core):

  • Additional functionality:
    • GravyScore (Grand Average of Hydropathy) as additional amino acid property

• BioFSharp.IO:

  • Additional functionality:

    • GAF Parser for GO Annotation file format: Gene Association File
    • Uniprot style Fasta header parser
    • FastA to GFF3 converter functions
    • GFF3 Pretty Printer

  • BugFixes:

    • Fix OboParser just taking the last occurence of the alt_id keyword and discards previous ones.
    • Fix Fasta and GFF3 writers appending to files instead of recreating

• BioFSharp.BioTools:

  • Additional functionality:

    • TMHMM biocontainer API wrapper (TMHMM 2.0c predicts transmembrane helices in proteins)
    • FastP and Hera biocontainer API wrapper
    • IntaRNA biocontainer API wrapper (IntaRNA is a tool for prediction of various nucleotide interactions)

  • BugFixes:

    • Fix Stream entry closed error in BioContainer.tarOfStream()

• BioFSharp.ImgP:

  • Additional functionality:

    • update 3DCWT correlation calculation to loop

  • Bugfixes:

    • fix height adjustment in ricker
    • fix Ricker values for discrete time points

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

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