Code, Tools, Software

OctocatWe’re on GitHub!



Biocode Commons

TIP: BNHM Students and Staff, you are eligible for a educational upgrade at GitHub including 5 free private repositories. Sign up here.

Looking for Bioinformatics pipeline?

Bioinformatics pipeline scripts from Berkeley researchers:


Pipeline for Illumina SCPP experiment data, exon capture, and transcriptome sequence data

Computational Genomics Resource Laboratory (CGRL)- QB3

Ke Bi’s scripts for QB3

Dan Portik

Author of SUPERCRUNCH for Phylogenetic Data and other python scripts for alignment, exon coverage, and bioinformatics tasks

Tyler Linderoth

various scripts for NextGenSequencing work

Species mapping and distribution modeling, analysis

Biodiversity Informatics Training Workshop tutorials and examples
MVZ’s Bio-GIS portal

Web Services for Biodiversity Data

Ecoengine API- documentation and examples here
Discover the current Ecoengine Datasets

ESRI ArcGIS for BNHM users

Access installation information here if you have a password. Contact for more information.

Other UC Berkeley Resources

Code at Berkeley

A version control service available to campus software development teams which facilitates the creation and administration of centrally supported Subversion repositories.


Everyone needs a bibliography manager. Consider free, opensource Zotero if you are not already using it. If you are the Library has ways Berkeley users can sync their library attachments to their Berkeley Box account via Webdav.