The WWW Virtual Library: Model Organisms

This site is a catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. Other organisms are listed under the Virtual Library sections for Genetics and Developmental Biology.

To comment on the site or suggest links, please contact the maintainer. If you would like to take over responsibility for a specific Model Organism, please contact the Virtual Library.

What is a Model Organism?

Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information.

General Model Organism Resources

There is little on the web regarding model organisms in general, but some of the better resources are:

Report of a 1998 NIH workshop on Model Organism databases
Functional and Comparative Genomics from the Human Genome Project talks about the genomes of model organisms, and how they relate to the human genome.
NIH reference site for model organisms, with links and information on grants and programs.
The GenomeWeb has extensive links for genomics of various organisms.
MEOW allows searches on genes of all major model organisms and human through a single interface.
Use of model organisms in teaching biology.

Comparative Genomics of model and other organisms

With many genomes now sequenced, there are several efforts to functionally link genes in model organisms with their counterparts in humans and other models to expand their utility as models of human genes and processes. Some resources include

The Gene Ontology Consortium (GO) aims to classify broad and specific functions of genes across several organisms.
An oldish (1997) list of human disease genes and their model organism counterparts, at XREFDb, a project to link model organism genes to human homologs.

What are the main Model Organisms?

There are other excellent sections in the Virtual Library for these major Model Organisms:

E. coli (bacterium)
Yeasts (Saccharomyces cerevisiae, and other species)
Dictyostelium discoideum (slime mold)
Drosophila melanogaster (fruit fly)
Xenopus laevis (African clawed frog)

The following are the most popular web resources for other major model organisms.

Caenorhabditis elegans (nematode worm)

This tiny worm has a very fast life cycle, an invariant lineage (every animal has a specific number of cells) and is the first multicellular animal to have it's genome sequenced.

An introduction to the worm, from the Riddle lab, and a more technical introduction from Mark Blaxter and another from the Minnesota Genetics Center.
The C. elegans WWW server by Leon Avery at UTSMC is the best online reference for C. elegans, including an introduction, a list of worm labs and a search engine for worm literature.
Wormbase is a large-scale database covering information on all worm genes.
The full genome of has been sequenced (Sanger Center and Washington University)
The C. elegans EST sequencing and expression mapping project (NEXTDB) from the Kohara lab.
A consortium of labs aims to create knockouts of every worm gene.
ACeDb is a complex but powerful database of C. elegans genetic information. A web interface is avaible from the USDA.
The worm stock center (Caenorhabditis Genetics Center in Minnesota).
WormAtlas is a database of structural and behavioral anatomy of the worm.
Worm protocols from the Ambros lab.
The bionet.celegans newsgroup, with an introduction and archive at the UTSMC site.
Other nematodes are covered by Wormland.
A good links page from the Ward lab.
elegansNet: links on C. elegans and an eclectic variety of other biological topics. Heavy use of frames. Includes extensive introductory links (ACekit)

Arabidopsis thaliana (mustard plant)

This is now the main model plant system for genetics. Its small genome, and the recent application of classical genetics has put it far ahead of other models of agricultural importance (tomato, tobacco, corn etc.) It's genome is due to be fully sequenced in 2000.

Arabidopsis thaliana database (AtDb): Major database on Arabidopsis genes and genomics efforts, with additional information on Arabidopsis researchers.
cDNA sequencing project: Major EST sequencing project from the University of Minnesota and Michican State University.
Arabidopsis database at TIGR: Genome and EST sequences from TIGR, including their "Gene Index" compilation of ESTs and genomic data into putative gene sequences.
Stock Centres: Wild type and mutant stocks are available from Ohio State University and the University of Nottingham in England. See also the Lehle seeds company catalog.
Extensive list of Arabidopsis labs on the web, from Lehle Seeds.
News and information: Lots of up-to-date community information from arabidopsis.com.
WeedsWorld, the Arabidopsis community newsletter is archived from 1994-97.
Arabidopsis also has mailing lists and a newsgroup, bionet.genome.arabidopsis, which is archived.
Arabinet at Harvard is a good collection of links.
MIPS genome project in Germany offers sequences, annotations and functional classification.

Zebrafish

This small fish is a relatively new model. As a vertebrate, it is a good model for aspects of human biology, but is cheaper and easier to handle than mice, as well as having a transparent and readily accessible embryo for developmental biology work.

FishNet at University of Oregon is an extensive resource site.
The Zebrafish information server is another excellent general resource from the University of South Carolina.
Washington University has a Zebrafish EST sequencing project underway.
The ZebraFish Webserver at the Driever Lab covers anatomy, microsatellite maps and YAK libraries.

Mouse

The closest model organism to humans is especially used in development, genetic and immunology studies.

The Whole Mouse Catalog has an extensive set of references to information throughout the web.
Mouse Knockout Database (BioMedNet). Atlas of phenotypes and other information for mouse genes which have been disrupted (commercial).
Genetic and Physical maps of the Mouse genome (MIT)
The Mouse Atlas and Gene Expression Database
- Atlas of the Mouse Brain: scans through wild-type and mutant mouse brains.
Mouse Genome Informatics: combination of databases at Jackson labs: the Mouse Genome Database (MGD), the Gene Expression Database, and the Encylopedia of the Mouse Genome, a Mac genome map viewer, which together give extensive coverage of mouse genetics and genomics.
The TBASE database of transgenic mouse strains, from the Jackson lab.
An article on Mice in Cancer Research.
Human/Mouse homology maps, from NCBI.
Mouse Genome Resources from NCBI.

Other model organisms

Unicellular

Chlamydomonas reinhardtii, a unicellular alga.: Chlamydomonas internet resources from Wallace Marshall.
Cyanobacteria, (photosynthetic bacteria).: Cyanosite

Plants

Maize: The Maize Page at Iowa State University.; Maize Genetics sites of interest; MaizeDB, the maize genome database.
Trees: The Virtual Library on Forest Genetics and Tree Breeding.

Invertebrates

Aplysia californica: a snail used in Neurobiology research: The Aplysia hometank (Cornell)
Ascidians: Primitive chordates used in developmental biology: US Ascidian Home page (Fullerton)
Cnidarians/Coelenterates (jellyfish, corals, hydra etc.): Cnidaria home page
Sea Urchin: Urchin Web; UrchiNet database
Mosquito (Aedes sp.): Mosquito Genomics Server

Vertebrates

Fugu rubripes: Pufferfish with a very compact genome, used in genomics research. The genome is now largely sequenced and being assembled.: Good Fugu site at the DOE JGI; Fugu pages at the MRC in England.
Medaka (ricefish; Oryzias latipes): another genetic model fish: Medakafish Homepage
Assorted mammals (mostly genomic resources): Roslin Institute: Mapping databases for Pig, Chicken, Sheep, Cattle, Horse, Cat and Tilapia (fish).; The Dog Genome project at Berkeley.; US Department of Agriculture genome mapping projects for Sheep, Pig and Cow.

Other Model Organism Pages

Sanger Center list of MO databases
Another one at Caltech
A nice review of model organism sites by Pam Gannon, for HMS Beagle (also available here).
Genomes and Organisms, an extensive list at Infobiogen.
Cybergenome.com has links for model organisms and humans.
Functional Genomics links from Science Genetics links from Nature.

(Belorussian translation )

http://ceolas.org/VL/mo/
By Gerard Manning
Last update: Oct 14, 2010