RELEASE_NOTES.md

2.0.0 - tbd

All packages now target netstandard2.0 as lowest common denominator.

Additions:

• BioFSharp:

  • [Breaking] Conversion extensions for BioCollections
  • [Breaking] Tagged Sequence and Phylogenetic Tree have been reworked as top level types
  • Add functionality to construct phylogenetic trees from clustered data or raw sequence data

• BioFSharp.BioContainers

  • BLAST biocontainer :
    • full blastn, blastn-short, megablast, and dc-megablast DSLs
    • [Breaking] full blastp, blastp-fast, and blastp-short DSLs
  • TargetP BioContainer :
    • Add functions to run the container with a mounted directory
  • Add TargetP2 BioContainer API

• BioFSharp.IO:

  • OBO parser: Extended term parser for spec 1.4
  • OBO parser: fix (#111)[#111]
  • SOFT parser now parses Data tables
  • OBO Parser: add verbosity settings (#129)
  • ADD DSSP and Stride parsers
  • ADD PDB Parser (only some records supported))

Bugfixes:

• BioFSharp:

  • Fix stack overflow on Phylogenetic tree construction based on hierarchical clusters

• BioFSharp.IO:

  • OBO parser now correctly parses lists of relationships
  • [Breaking] FastA.writeToStream is now correctly typed and does not close the stream after writing
  • SOFT parser now parses sample_label / sample_label_protocol correctly
  • Fix fasta writer using UTF8BOM encoding ((#116)[#116])
  • Fix newick writer missing leaf case

1.2.0 - Monday, March 30

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)

1.1.0 - Monday, March 23, 2020

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](https://github.com/CSBiology/BioFSharp/pull/83/commits/615dcbfd30632d6fdf7a70edae9f5227ce250937)

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

0.0.15 - Thursday, March 7, 2019

• 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.
• Othert additions:
  • BioFSharp.BioTools:
    • Integration of new tools as biocontainer APIs:
      • Hera
      • FastP
      • ClustalO
      • HMMER (experimental):
        • hmmbuild
        • hmmalign
        • hmmsearch
        • hmmscan
        • hmmemit
        • hmmpress
        • hmmconvert

0.0.14 - Tuesday, February 12, 2019

• Addition of blast biocontainer support for makeblastdb, blastp, blastn with full parameter wrapping
• Extension of 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)

0.0.13 - Friday, February 8, 2019

• Addition of the BioTools project, which 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

0.0.12 - Friday, December 28, 2018

• Addition of Pretty Printers, SOFT Parser, GEOFTP functions
• Improvement and refactoring of Modification functionality

0.0.11 - Tuesday, November 2, 2018

• ImgP - project introduction

0.0.1 - Thursday, August 9, 2018

• Initial release