Resources/Links

If you think an important link is missing, please send an email to BMCDB.UCDavis@gmail.com with the link and a short description of what you use it for.

UC Davis
UC Davis
College of Biological Sciences
BMCDB Graduate Group
Designated Emphasis in Biotechnology
Graduate Studies
Graduate Studies Forms
Graduate Studies Handbook
Registrar’s Office
Graduate Students Association (GSA)
BMCDB Application link (please read carefully)
MCB124 – proteins and nucleic acid: structure and function
MCB221A – protein and structure resources

Literature Search
PubMed
PubMed VPN log-in (UC Davis only)
Google scholar
Digital Object Identifier
Web of Knowledge

General Biology
StarGenetics
Microscopy basics and practical info
Design PCR primers
NEB cutter v.2 – restriction mapping tools
Promoter identifier (cloning)

Bioinformatics
CoGe – Comparative Genomics Platform
GO – gene ontology
BLAST homepage
BLASTn – search a nucleotide database using a nucleotide query
BLASTp – search protein database using a protein query
BLASTx – search protein database using a translated nucleotide query
tBLASTn – search translated nucleotide database using a protein query
tBLASTx – search translated nucleotide database using a translated nucleotide query
blast2seq
clustalW

Metabolics / Metabolome

MetaboAnalyst

KEGG
MetaCyc – Metabolic Pathway database
MetPA – web-based metabolomics tool for pathway analysis & visualization
HMDB – human metabolome database
AraCyc – Arabidopsis metabolic pathways

Databases
SGD – Saccharomyces Genome Database
NCBI Trace Archive
NCBI SRA
DDBJ
EMBL-EBI
High resultion mass spectral database
ChemSpider – linking compound info across the web
PubChem Compound

Teaching Resources

Star Genetics

Star BioChem

MIT Open Courseware: Biology

Protein Structure / Viewers
RasMol
PDB files
Jpred3 – secondary structure predictor
Dali server – find proteins by structure similarity

Protocols/Methods
Protocol-Online
Nature methods
Cold Spring Harbor Protocols
Yeast protocols

Writing tools
endnote
Mendeley – free reference manager
Grant writing editorial
The Writer’s Handbook – grammar and punctuation

Data visualization
Circos – circular data visualization package (online + Perl code)
Wordle – word-cloud software

Genome browser
UCSC Browser
CoGe – Comparative Genomics Platform
Ensembl
TAIR – Arabidopsis thaliana genome browser
Saccharomyces cerevisiae genome browser

Flow Cytometry

FlowJo

Purdue List

Programming
Phyton progamming language
C++ programming language
C++ tutorial
Perl – progamming language
Perl & Unix Primer for Biologist (UC Davis – Korf Lab)
R – statistical and visualization software package
learn R – Phylogenetic workshop 2010 (UC Davis – Wainwright lab)
Quick-R – learn basic graphical R skills

Mass Spectrometry
Scientific Instrument Services – Mass Spec tools

Free software for PC
AMDIS – Automated Mass Spectral Deconvolution and Identification System
XCMS (with XCMS2) – mass spectrometry analysis software
MZmine 2 – mass spectrometry data processing