Question: Notable open source bioinformatics projects written in Java?
2
gravatar for kam.stratos
3.0 years ago by
kam.stratos20
kam.stratos20 wrote:

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.

java bioinformatics software • 1.2k views
ADD COMMENTlink modified 4 months ago by RamRS20k • written 3.0 years ago by kam.stratos20

I think SourceForge is going out of fashion and it's being overcome by Github.

ADD REPLYlink modified 5 months ago by RamRS20k • written 3.0 years ago by dariober9.9k

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

ADD REPLYlink modified 5 months ago by RamRS20k • written 3.0 years ago by kam.stratos20
10
gravatar for Pierre Lindenbaum
3.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

... Edit and using the seqanswer wiki.

ADD COMMENTlink modified 5 months ago by RamRS20k • written 3.0 years ago by Pierre Lindenbaum116k

That edit is a thread killer. Thanks!

ADD REPLYlink modified 5 months ago by RamRS20k • written 3.0 years ago by kam.stratos20
6
gravatar for genomax
3.0 years ago by
genomax62k
United States
genomax62k wrote:
ADD COMMENTlink modified 5 months ago by RamRS20k • written 3.0 years ago by genomax62k
5
gravatar for dariober
3.0 years ago by
dariober9.9k
Glasgow - UK
dariober9.9k wrote:
ADD COMMENTlink modified 5 months ago by RamRS20k • written 3.0 years ago by dariober9.9k
2
gravatar for Philipp Bayer
3.0 years ago by
Philipp Bayer5.9k
Australia/Perth/UWA
Philipp Bayer5.9k wrote:
ADD COMMENTlink modified 5 months ago by RamRS20k • written 3.0 years ago by Philipp Bayer5.9k
2
gravatar for Dan D
3.0 years ago by
Dan D6.7k
Tennessee
Dan D6.7k wrote:

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.

ADD COMMENTlink modified 5 months ago by RamRS20k • written 3.0 years ago by Dan D6.7k
2
gravatar for mkulecka
3.0 years ago by
mkulecka300
European Union
mkulecka300 wrote:
ADD COMMENTlink modified 5 months ago by RamRS20k • written 3.0 years ago by mkulecka300
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