Bioinformatics

NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

European Bioinformatics Institute EBI

The European Bioinformatics Institute (EBI) is a non-profit academic organisation that forms part of the European Molecular Biology Laboratory (EMBL). The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.

DNA Data Bank of Japan DDBJ

DDBJ is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences from researchers and to issue the internationally recognized accession number to data submitters. They collect data mainly from Japanese researchers, but accept data and issue the accession number to researchers in any other countries. Because they exchange the collected data with EMBL/EBI and GenBank/NCBI on a daily basis, the three data banks share virtually the same data at any given time.

Universal Protein Resource (UniProt)

is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt has three components, each optimized for different uses. The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Reference Clusters (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences.

Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (RCSB PDB)

The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. This site offers tools for browsing, searching, and reporting that utilize the data resulting from ongoing efforts to create a more consistent and comprehensive archive.

Metabolomics

Metabolic Network Exchange (MetNet)

MetNet is emerging software to visualize, explore, statistically analyze and model mRNA, protein, and metabolite profiling data in the context of a metabolic and regulatory network map of Arabidopsis.

 

BioCyc Database Collection (BioCyc)

The BioCyc collection of Pathway/Genome Databases (DBs) provides electronic reference sources on the pathways and genomes of different organisms. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received.

Systems Biology

Cytoscape (Cytoscape)

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

MapMan (MapMan)

MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.