The idea is to have a list of communities and write a short paragraph about them. Moreover, we can contact each of them to get opinions and solve: #9 i.e. interest in getting examples included from more different communities
- Galaxy
- GalaxyP
- IUC
- BioJS (community paper)
- BioConductor
- BioJava
- BioRuby
- BioNode
- BioPython
- BioSQL
- BioPerl
- EMBOSS
- BioMoby
- GMOD
- Homebrew
- Homebrew-science
- mothur
- Open Babel
- RDKit: Open-Source Cheminformatics Software
- Arvados
- Big Data Genomics
- Fiji
- scikit-learn
- SequenceServer
- SciRuby
- Software Carpentry
- [Data Carpentry] (http://datacarpentry.org/)
Please feel free to add more.
Several of the communities listed above were added by looking at the list of main projects of the Open Bioinformatics Foundation
And Wikipedia also has a list of open-source Bioinformatics software