Resources for Reseachers

UC Davis
UC Davis

Robert Mondavi Institute

Viticulture & Enology Department

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
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

Protein Structure / Viewers
RasMol
PDB files
Star Biochem
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

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

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s