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http://www.wholecellkb.org/

A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: * Their subcellular organization, * Their chromosome sequences, * The essentiality, location, length, direction, and homologs of each gene, * The organization and promoter of each transcription unit, * The expression and degradation rate of each RNA gene product, * The specific folding and maturation pathway of each RNA and protein species including the localization, N-terminal cleavage, signal sequence, prosthetic groups, disulfide bonds, and chaperone interactions of each protein species, * The subunit composition of each macromolecular complex, * Their genetic code, * The binding sites and footprint of every DNA-binding protein, * The structure, charge, and hydrophobicity of every metabolite, * The stoichiometry, catalysis, coenzymes, energetics, and kinetics of every chemical reaction, * The regulatory strength of each transcription factor on each promoter, * Their chemical composition, and * The composition of its typical SP-4 laboratory growth medium. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. Users can download the WholeCellKB source code and content to create and customize - including the content, data model, and user interface - their own model organism database.

Proper citation: WholeCellKB (RRID:SCR_004104) Copy   

•   Source: SciCrunch Registry

http://mass-spec.stanford.edu

Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development.

Proper citation: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility (RRID:SCR_017801) Copy   

•   Source: SciCrunch Registry

http://www.pharmgkb.org/

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

Proper citation: PharmGKB (RRID:SCR_002689) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/nusselab/cgi-bin/wnt/

A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year.

Proper citation: Wnt homepage (RRID:SCR_000662) Copy   

•   Source: SciCrunch Registry

http://www.yeastgenome.org/

A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available.

Proper citation: SGD (RRID:SCR_004694) Copy   

•   Source: SciCrunch Registry