Resources

su.class.cs279 - This forum enables students to discuss problems that they encounter. It is also an excellent place to find a group for the project. For information on how to access and use class newsgroups see A Stanford Intro to Usenet .

Kimball's Biology Pages - Huge index of information on many specific biological topics

Tools

NCBI BLAST - Web-based interface for aligning nucleotide or protein sequences

UCSC Genome Browser and Ensembl - Browse the genomes of sequenced organisms while viewing many different types of annotations

Cytoscape - Program for visualization and analysis of molecular interaction networks

Graphviz - Program for visualization of general graphs

Grasper - Suite of tools for working with graphs

Graemlin - Multiple alignment of protein interaction networks

MOMA - Analysis of optimality in natural and perturbed metabolic networks

UCSD System Biology Downloads - Software tools for flux balance and extreme pathway analysis

VisANT - Visual Analysis Tool for Biological Networks and Pathways

Databases

The Gene Ontology (GO) - A controlled vocabulary for describing genes

KEGG - Databases of known pathways, genes, and reactions

Reactome - A pathway database

COG - Classification of proteins based on phylogenetic relationships

STRING - Search Tool fort he Retrieval of Interacting Genes/Proteins

SCOP - A hierarchical database of protein families organized based on structure

Stanford MicroArray Database - Repository of microarray experiment data

Metacyc - Database of metabolic reactions for 600+ organisms

UCSD Systems Biology Reconstructions - High-quality reconstructions of several network types for a few organisms.

ENZYME - An enzyme nomenclature database

Brenda - Large database of enzymes with functional information

DIP - Database of interacting proteins

MINT - Molecular interactions database with a focus on known protein interactions from the literature

Saccharomyces Genome Database - Huge database of information on Saccharomyces (yeast) genomes

NCBI Gene Expression Omnibus - NCBI's database of expression data

The BioGRID - A repository for various types of biological interaction datasets

Resources for Fungal Comparative Genomics

InterDom - Database of putative interacting proteins

Datasets

Segal Lab datasets - Annotation and expression datasets from Eran Segal's lab

Flux Measurements

See supplementary data from:

Blank, L. M., Kuepfer, L., and Sauer, U. 2005. 13 C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 6: R49.

Kuepfer, L., Sauer, U., and Blank, L. M. 2005. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res. 15: 1421-1430.