Arkin Laboratory

BioE142 Bugzilla

BioE142 CVS

BioE142 Discussion

Data and Databases

Name	Description
Physical Properties of Amino Acids	A list of imporant properties of amino acids. Can be used to calculate hydropathy plots, identify surface properties of proteins, calculate theoretics 2D gels, etc.
Expasy	A large collection of sequence, structure, pathway,etc. databases and tools. A central resource for many biologists
RCSB	Protein and Nucleotide Structure Databse. A central resournce.
NCBI	Sequence, Structure, Taxonomy, Literature, etc. A central resource
KEGG	The Kyoto Encyclopedia of Genes and Genomes. An interesting pathway database.
Brenda	A comprehensive data of enzyme properties.
WIT, EMP	Very interesting comparative genomics databases with deep pathway information.
SMA	The Stanford Microarray Database
Wormbase	A community built database of things nematodish.

 

Tools

Name	Description
EMBL's List of Tools	A well organized and accessible list.
TIGR's Compendium	Many good tools developed by the most prolific sequencer of microbial genomes.
Pedro's Biomolecular Research Tools	A large annotated list of software tools for molecular biology

 

Collections and Companies

Name	Description
Proteome	One of the best annotators for eukaryotic proteins and genes.
DoubleTwist	One of the canonical bioinformatics companies that has a location nearby.
Informax	Software developer with a large market share. Good downloadable tools.

 

Standards and Conventions

Name	Description
GeneOntology Consortium	Standards for Classification of biological Data
XML	Standards and DTD's for different XML definitions. Many biological ones here.
WWW	The world-wide web standards site. Very useful.
OpenBio	A group trying to set standards for the use of Perl, XML, Java, etc.l in bioinformatics. There be code here!
MGED	The microarray gene expression data group's standards page.

Online Tutorials

Name	Description
Some Perl Stuff	Private Perl Documentation