We’re on GitHub!
Find our BNHM tools on Github
R Shiny Deployments
ReserveMapper
Ecoreader
BerkeleyMapper
Biocode
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.
Zotero
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.