IBM Computional Biology

• IBM Research Computational Biology Center
• IBMHealthcare and Life Sciences
• Online web lectures include gene expression array analysis lecture
• Blue Gene
• SHAMAN/Integrated Medical Records

Bioinformatics tools and databases

• NCBI, National Center for Biotechnology Information
• PubMed, a database of biomedical literature
• GenBank
• IBM Bioinformatics & Pattern Discovery Group
• ExPASy Molecular Biology Server
• Stanford Microarray Database
• MIPS: Munich Information Centre for Protein Sequences
• KEGG: Kyoto Encyclopedia of Genes and Genomes
• ExpressDB RNA Expression Database
• TIGR: The Institute for Genomics Research
• The EMBL/EBI Outstation, European Bioinformatics Institute
• Biomax, Inc.

Yeast (Saccharomyces cerevisiae) databases

• PathCalling Yeast Interaction Database
• Yeast Cell Cycle Analysis Project
• SGD, Saccharomyces Genome Database

Functional genomics and proteomics databases

• DIP: Database of Interacting Proteins
• BIND: The Biomolecular Interaction Network Database
• ERGO from Integrated Genomics, Inc.

Cellular Signalling and Pathway Mapping

• Signalling Gateway - Alliance for Cellular Signaling
• Iyengar Laboratory
• Cytoscape

Integrative modeling and simulation

• Physiome Project
• Systems Biology Software at the Keck Graduate Institute
• Virtual Cell Project of The National Resource for Cell Analysis and Modeling
• E-Cell Project
• Microbial Cell Project
• World Wide Web Instructional Committee Virtual Cell
• Entelos, Inc.
• Gene Network Sciences, Inc.

Standards

• MAML, a standard for DNA-array experiment annotation and data representation
• Gene Ontology Consortium, a vocabulary for eukaryotic genes and protein rolesGEML, a standard for exchanging gene expression data
• SBML, a standard for systems biology
• CellML, a standard for biological modeling
• BioUML