Notable open source bioinformatics projects written in Java?
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6.8 years ago
kam.stratos ▴ 20

I'm a Computer Science undergraduate writing my thesis which is about analyzing open source bioinformatics projects and extracting standalone modules. I need those projects to be written in Java and preferably be stable or mature. So far I've found a bunch of projects via SourceForge and I was wondering if there are any notable ones that are not hosted there. A different repository that has a bioinformatics category would be helpful too.

Here's a list of the most promising projects I have so far:

  • Jenetics
  • JGap
  • Jmol
  • Juicebox
  • Picard
  • RDP Classifier
  • Shim
  • Tassel
  • The Chemistry Development Kit
  • Toxfree
  • TreeView
  • VarScan

Thanks in advance.

software java bioinformatics • 2.1k views
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I think SourceForge is going out of fashion and it's being overcome by Github.

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I agree, but it does have a "bioinformatics" category and supports filtering based on project maturity. Thanks for your suggestions below.

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That edit is a thread killer. Thanks!

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6.8 years ago
GenoMax 123k
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6.8 years ago
Dan D 7.3k

JEnsembl is a JAVA API for Ensembl.

Contrail and Cloudbase are assemblers. The latter got some new life when an enterprising programmer retooled it for GPUs.

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mkulecka ▴ 340
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