We’re on GitHub!
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.
PRO TIP: How to cite your code with a DOI? UC Library has a step-by-step guideline to generate a citable DOI for your code hosted on Github with Zenodo.
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 –
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 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, 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.
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