Resources for Reseachers

UC Davis
UC Davis

Robert Mondavi Institute

Viticulture & Enology Department

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

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

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

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

SGD – Saccharomyces Genome Database
NCBI Trace Archive
High resultion mass spectral database
ChemSpider – linking compound info across the web
PubChem Compound

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

Nature methods
Cold Spring Harbor Protocols
Yeast protocols

Writing tools
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
TAIR – Arabidopsis thaliana genome browser
Saccharomyces cerevisiae genome browser

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

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