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BioJava is an open-source project dedicated to providing a Java framework for processing biological data.
Java Other

Merge pull request #304 from sbliven/master

Updating SCOPe to version 2.05
latest commit f069b4f084
@andreasprlic andreasprlic authored
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biojava-aa-prop [maven-release-plugin] prepare for next development iteration
biojava-alignment [maven-release-plugin] prepare for next development iteration
biojava-core Merge branch 'master' into minor
biojava-genome Patched to allow tests to be completed on windows. It was due to the …
biojava-integrationtest Reverting parser change: removing pure non-poly chains is a bad idea.
biojava-modfinder [maven-release-plugin] prepare for next development iteration
biojava-ontology [maven-release-plugin] prepare for next development iteration
biojava-phylo [maven-release-plugin] prepare for next development iteration
biojava-protein-comparison-tool fixing wrong version number
biojava-protein-disorder [maven-release-plugin] prepare for next development iteration
biojava-sequencing [maven-release-plugin] prepare for next development iteration
biojava-structure-gui Fix bug with flexible MultipleAlignments
biojava-structure Merge pull request #304 from sbliven/master
biojava-survival [maven-release-plugin] prepare for next development iteration
biojava-ws [maven-release-plugin] prepare for next development iteration
development Add addlicense.sh script
.gitignore ignore *~ files
.travis.yml adding new parameter to support new Travis container-based infrastruc…
KEYS updating my code signing key
LICENSE moving the last ant based trunk to a branch
ignore.txt moving the last ant based trunk to a branch
pom.xml updating dependencies to latest versions.
readme.md updating to v 4.1.0

readme.md

Welcome to BioJava

Build Status Dependency Status Version License

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

Please visit our homepage.

Documentation

The BioJava Cookbook is a collection of simple examples that teach the basics for how to work with BioJava. We are also working on a tutorial for biojava (currently only for protein structure modules).

Maven Repository

The Maven Repository contains the jars of all releases, as well as SNAPSHOT builds of the latest code base.

Quick Installation

If you are using Maven you can add the BioJava repository by adding the following XML to your project pom.xml file:

    <dependencies>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-core</artifactId>
        <version>4.1.0</version>
      </dependency>
      <!-- other biojava jars as needed -->
    </dependencies>

Snapshot builds

To use the latest builds from BioJava, you can add the following config your project's pom.xml:

<repositories>
    <repository>
      <id>oss.sonatype.org-snapshot</id>
      <url>http://oss.sonatype.org/content/repositories/snapshots</url>
      <releases>
        <enabled>false</enabled>
      </releases>
      <snapshots>
        <enabled>true</enabled>
      </snapshots>
    </repository>
  </repositories>

Mailing Lists

BioJava has two main mailing lists. In order to avoid SPAM both lists only accept postings from list members. Anybody can become a list member, so please subscribe before you post. If you send without being subscribed your mail might get stuck in the moderation loop, which can cause several weeks of delay (no fun to read through all that spam).

biojava-l general discussion list

This list is intended for general discussion, advice, questions, offers of help, announcements, expressions of appreciation, bugs found in release code and requests for features.

biojava-dev developers list

This list is intended for more technical discussions about API design, bugs in git development code, performance issues and things that might not be of interest to the more casual user.

Please cite

BioJava: an open-source framework for bioinformatics in 2012
Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis
Bioinformatics (2012) 28 (20): 2693-2695.
doi pubmed

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