ST NetWatch: Model Organisms

Mustard plant, Arabidopsis thaliana: The Arabidopsis Information Resource (TAIR)
By the Carnegie Institution of Washington Department of Plant Biology and the National Center for Genome Resources (NCGR), TAIR covers sequencing initiatives, the Arabidopsis database, maps, stocks, protocols, nomenclature, meetings, microarray data and more. This site succeeds the Arabidopsis thaliana Database Project (AtDB).
Nematode worm, Caenorhabditis elegans: The C. elegans Genome Project
Sequence data, annotated genomics, ESTs, predicted proteins, and knockouts. Produced by the Sanger Centre.
Nematode worm, Caenorhabditis elegans: WormBase
To get genetic maps, information about mutant phenotypes, and sequence information from C. Elegans, WormBase is the place to go. "WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes." The site is updated every few weeks.
Nematode worm, Caenorhabditis elegans: WormBook
WormBook, a companion to WormBase, is a collection of reviews on almost every aspect of C. elegans biology. Reviews are organized into sections such as “Disease Models and Drug Discovery” and “Neurobiology and Behavior” that contain peer-reviewed chapters authored by leading researchers. The section titled “Signal Transduction” includes reviews on receptor tyrosine kinase signaling, heterotrimeric guanine nucleotide-binding proteins (G proteins), chemoreception, and developmental signaling pathways such as those mediated by Wnt and Notch. Signaling information is not limited to this section but can be found throughout the book, with signaling pathways discussed in cell biological contexts such as adhesion, cell cycle regulation, and intracellular trafficking. The site also includes a discussion forum and a collection of laboratory protocols called WormMethods.
Slime mold, Dictyostelium discoideum: dictyBase
dictyBase is an integrated genetic and literature database that contains published Dictyostelium discoideum literature, genes, expressed sequence tags (ESTs), as well as the chromosomal and mitochondrial genome sequences. Direct access to the genome browser, a Blast search tool, the Dictyostelium Stock Center, research tools, colleague databases, and much much more are just a mouse click away. dictyBase is funded by a grant from the National Institute for General Medical Sciences.
Fruit flies, Drosophila: FlyBase
According to Groucho, "Time flies like an arrow, and fruit flies like a banana." This may be the only Drosophila-related information you won't find at FlyBase -- the premiere effort to create and maintain an exhaustive, curated model organism database. Maps, genes, transposons, aberrations, stocks, references, people and more -- its all here.
Fruit flies, Drosophila: The Interactive Fly
This site provides continuously updated information relating to Drosophila genes and their roles in development. The information is well-organized and cross-referenced to FlyBase. Other useful components of the site are images of developing Drosophila and detailed descriptions for most of the genes in the database.
Mouse, Mus musculus: EMAP: The e-Mouse Atlas Project
The e-Mouse Atlas Project is a gateway to EMA, the e-Mouse Atlas, and EMAGE, the e-Mouse Atlas of Gene Expression. EMA is an anatomy atlas that shows 3D reconstructions and sections of the mouse during every stage of development. There are also special topics for some stages, such as limb or organ development, information on staging conventions, and the criteria for assigning stages to embryos. EMAGE is a database of spatial gene expression patterns sorted by developmental stage and includes tools for analyzing the data contained in the database. The Spatial Search tool allows users to highlight an area from a section or whole-mount image of any stage to identify genes expressed in that region at the selected stage. With the Gene and Pathways search tools, users can search for expression patterns by entering a sequence, gene name, or KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway definition to see expression patterns of genes involved in a specific signaling pathway or biological process, such as osteoclast differentiation or acute myeloid leukemia. Information about the molecular interactions in each biological or signaling pathway is provided, and results are sorted by developmental stage. Genes that are coexpressed with a gene of interest or expressed in a specific tissue or at a developmental stage of interest may be identified with the Similar Patterns search tool. EMAP is produced by the Medical Research Council and the University of Edinburgh in collaboration with the Jackson Laboratory and Heriot-Watt University.
Mouse, Mus musculus: Mouse Genome Informatics
The Jackson Laboratory’s Mouse Genome Informatics (MGI) site includes extensive information on strains, mutant phenotypes and disease models, gene function, and biochemical pathways. The Gene Expression Database (GXD) can be searched by gene, tissue, or developmental stage. In addition to information on individual genes and alleles, the site also includes the Mouse Genome Browser (MGB) and tools for exploring the genome through linkage maps, cytogenetic maps, and physical maps. Researchers may submit gene expression data or information about mutant strains and phenotypes to the database. The site includes the Mouse Tumor Biology (MTB) Database, a collection of information on spontaneous and induced tumors, strains engineered to develop tumors, tumor pathology, and information on the genetics of tumor susceptibility.
Rat, Rattus norvegicus: Rat Genome Database (RGD)
Like other organism-specific genome databases, the Rat Genome Database (RGD) exists to collect, manage, and distribute genetic, genomic, physiological, and strain information on one species—in this case, Rattus norvegicus. RGD contains the types of information you would expect from a model organism database—genome sequences, linkage maps, information on genes and gene products, gene expression data, and quantitative trait loci (QTL) mapping data. However, RGD also contains a wealth of information on rat physiology, detailed descriptions of strains and disease models, and a large collection of biochemical, signaling, and physiological pathway diagrams. Disease portals offer information on QTL, genes, and strains associated with rat models of cancer, diabetes, metabolic syndrome, and cardiovascular and inflammatory diseases. RGD provides free online tools for mining and analyzing the database contents, including a tool that can perform cross-species comparisons of genomic sequences between rat, mouse, and human. Many of the site's features are described in video tutorials that illustrate how to interact with the database and use the available tools, and there is a community forum where researchers can share information and advice. RGD is curated and maintained by a team at the Medical College of Wisconsin.
Yeast, Saccharomyces cerevisiae: Saccharomyces Genome Database (SGD)
SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The site offers many useful tools for finding information, especially the new SGD Resource Guide. Genetic information is available as maps, alignments, a table of every yeast gene with a plainly written description, microarray data sets (many of which relate to changes in gene expression in response to stimuli that activate signal transduction cascades). Protein analysis tools include alignment searching, searching functional analysis data projects, and homolog searching.
Yeast, Saccharomyces cerevisiae: Yeast Resource Center
The Yeast Resource Center site provides information to help researchers identify and characterize protein complexes in yeast. Tutorials on advanced technologies, such as mass spectrometry, yeast two-hybrid arrays, protein structure prediction, and deconvolution fluorescence microscopy, are accompanied by movies and protocols. A list of publications generated in collaboration with the Yeast Resource Center, an NCRR Biomedical Technology Resource Center, is available at the site, as is access to the Yeast Resource Center Public Data Repository, which provides data resulting from collaborations investigating Saccharomyces cerevisiae.
Frog, Xenopus laevis: Xenbase
Xenbase, the Xenopus laevis and Xenopus tropicalis Biology and Genomics Resource, was formerly known as the Xenopus Molecular Marker Resource (XMMR) and is curated and maintained by the laboratory of Peter Vize at the University of Calgary. This database includes data from both species because Xenopus laevis was used for many years as an experimental model before Xenopus tropicalis was adopted for laboratory use due to its shorter life cycle and smaller genome, making it more suitable for genetic studies and genome sequencing. The database includes a catalog of frog genes and gene expression patterns, a Xenopus tropicalis genome browser, a list of Xenopus-related publications, and information on developmental stages and anatomy. The Reagents and Protocols section offers lists of frog-specific antibodies, cDNA libraries, expressed sequence tags (ESTs), and technical information on plasmid vectors and phagemids used in frog research. Researchers can order strains, transgenic and mutant lines, clones, and transgenes from the Xenbase Stockcentre. The Community section contains information on people and labs in the Xenopus community, as well as job postings, workshops, and conferences. Community members can share protocols and information about frog genes, development, anatomy, and conferences in the Xenopus Wiki.
Zebrafish, Danio rerio: ZFIN: The Zebrafish Model Organism Database
This site is an online database for researchers working with Danio rerio, which has the advantage of translucent embryos ideal for visualization studies. The site provides information regarding zebrafish genetics, development, reference datasets, and connects the information to resources, such as probes and fish lines, available through ZIRC, the Zebrafish International Resource Center. In addition many community resources are also available, including educational materials for using zebrafish in the classroom and a wiki and newsgroup for maintaining communication among participants.
The WWW Virtual Library: Model Organisms
This site provides links to online resources for model organisms including E. coli, S. cerevisiae, Dictyostelium discoidium, C. elegans, Drosophila melanogaster, Arabidopsis thaliana, zebrafish, Xenopus laevis, mouse, sea urchin, and others.