OctocatWe’re on GitHub!

Find our BNHM tools on Github


R Shiny Deployments
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:

MVZseq– 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 – various python scripts for alignment, exon coverage, tasks
Tyler Linderoth – various scripts for NGS 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 BNHM@berkeley.edu 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, open-source Zotero if you are not already using it. If you are a Zotero user, the Library has guidelines for Berkeley users to sync their library attachments to their Berkeley Box account via Webdav.