https://github.com/bioscala/bioscala

Bioinformatics for the Scala programming language
https://github.com/bioscala/bioscala

Last synced: 23 days ago
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Bioinformatics for the Scala programming language

• Host: GitHub
• URL: https://github.com/bioscala/bioscala
• Owner: bioscala
• License: other
• Created: 2010-04-23T21:38:31.000Z (about 14 years ago)
• Default Branch: master
• Last Pushed: 2024-02-11T10:23:51.000Z (4 months ago)
• Last Synced: 2024-02-12T08:24:00.029Z (4 months ago)
• Language: Scala
• Homepage:
• Size: 308 KB
• Stars: 107
• Watchers: 16
• Forks: 20
• Open Issues: 1
• Metadata Files:
  • Readme: README
  • License: LICENSE

Lists

• AI - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning-cn - 官网
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learnings - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning-library - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-stars - bioscala
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-master - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)
• awesome-machine-learning - bioscala - Bioinformatics for the Scala programming language (Scala / General-Purpose Machine Learning)

README

        
The goal of the BioScala project is to create a scalable and functional

bioinformatics library; which can be used from Scala, Java, JRuby,

Jython and Clojure; building on existing libraries available on the JAVA

Virtual Machine (JVM), including BioJAVA and BioRuby.

This is the place for the BioScala project under the liberal BSD license.

See also the Tutorial

  http://monomorphic.org/bioscala/bioscala-tutorial.html 

design docs

  http://monomorphic.org/bioscala/bioscala-design.html 

and API docs

  http://monomorphic.org/bioscala/api/

This edition of BioScala has:

  - Strongly typed DNA, RNA Sequence, gapped and IUPAC ambiguous Sequence

  - Sequences contain lists of Nucleotide, AminoAcid, IUPAC, Gapped, Codon

  - Flexible Sequence user defined attributes

  - Transcription of DNA to RNA

  - Translation of (ambiguous) RNA to AA (using BioJava3)

  - Formats:

	  . Iterator based FASTA reader and writer

    . Iterator based PAML (PHY) file format reader

    . Phylip reader/writer (using BioJava)

  - Alignments and attributes (work in progress)

  - A translation example of calling into BioRuby

  - A tutorial in ./doc/tutorial.txt

BioScala uses the simple build tool (sbt) and behaviour driven development/unit

testing. See the INSTALL file for more information.

Please fork from https://github.com/bioscala/bioscala 

Pjotr Prins

Mailing list: http://lists.thebird.nl/listinfo.cgi/bioscala-thebird.nl

= INSTALL BioScala =

It is rather easy to install a working repository of BioScala. The JVM is

needed and sbt (simple build tool).

First download BioScala from github with:

  git clone http://github.com/bioscala/bioscala.git

Install Java. On Debian, for example:

  apt-get install openjdk-17-jdk

Install sbt (Simple build tool) from

  https://www.scala-sbt.org/

Install sbt and run it on the command line, for example

  # go to base bioscala directory

  cd bioscala

  # compile

  sbt compile

  # test

  sbt test

sbt will automatically download Scala and related jars. Then it will compile

and run the supplied tests.