Question: Notable open source bioinformatics projects written in Java?
2
gravatar for kam.stratos
3.4 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 • 1.4k views
ADD COMMENTlink modified 10 months ago by RamRS23k • written 3.4 years ago by kam.stratos20

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

ADD REPLYlink modified 10 months ago by RamRS23k • written 3.4 years ago by dariober10k

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

ADD REPLYlink modified 10 months ago by RamRS23k • written 3.4 years ago by kam.stratos20
10
gravatar for Pierre Lindenbaum
3.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

... Edit and using the seqanswer wiki.

ADD COMMENTlink modified 10 months ago by RamRS23k • written 3.4 years ago by Pierre Lindenbaum121k

That edit is a thread killer. Thanks!

ADD REPLYlink modified 10 months ago by RamRS23k • written 3.4 years ago by kam.stratos20
6
gravatar for genomax
3.4 years ago by
genomax70k
United States
genomax70k wrote:
ADD COMMENTlink modified 10 months ago by RamRS23k • written 3.4 years ago by genomax70k
5
gravatar for dariober
3.4 years ago by
dariober10k
WCIP | Glasgow | UK
dariober10k wrote:
ADD COMMENTlink modified 10 months ago by RamRS23k • written 3.4 years ago by dariober10k
2
gravatar for Philipp Bayer
3.4 years ago by
Philipp Bayer6.3k
Australia/Perth/UWA
Philipp Bayer6.3k wrote:
ADD COMMENTlink modified 10 months ago by RamRS23k • written 3.4 years ago by Philipp Bayer6.3k
2
gravatar for Dan D
3.4 years ago by
Dan D6.8k
Tennessee
Dan D6.8k 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 10 months ago by RamRS23k • written 3.4 years ago by Dan D6.8k
2
gravatar for mkulecka
3.4 years ago by
mkulecka300
European Union
mkulecka300 wrote:
ADD COMMENTlink modified 10 months ago by RamRS23k • written 3.4 years ago by mkulecka300
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