About EcoliHub

Sixty years of research have made Escherichia coli K-12 the most deeply understood organism at the molecular level. Much of what we know about cellular processes can be traced to fundamental discoveries in E. coli. In spite of its importance as a model organism, information about E. coli is distributed among many online resources. EcoliHub is being developed to make information now housed in multiple information resources, databases, and websites readily available to our user community. We envision a future where a dynamic community of online information and computational resources cooperate, with each resource focusing on its strength and expertise while linking to the strength and expertise of other resources. This vision of collaboration and sharing is part of a suite of strategies that are collectively referred to as Web 2.0.

EcoliHub will not replace existing information resources; the goal is to add value to these resources by:

The hub metaphor aptly describes our primary purpose; although a hub never touches the ground, without a hub the wheel will collapse. There are numerous resources with "rubber on the road," however they need a hub to pull them together into a well functioning whole. We are developing EcoliHub to be that hub. However, www.EcoliHub.org is not just a connecting point; it is a useful destination in its own right. We have listed below some of the services that we now provide, which is just the beginning of what we plan for the future:

1. A news and events system for keeping track of upcoming conferences and meetings
2. E. coli related news from public RSS feeds, blogs, and EPubs
3. A community forum where people can discuss experiments, ask about reagents, and connect prospective employers with prospective employees.
4. Cross-site search engine that identifies E. coli-specific information and distinguishes it from unrelated topics found by general search engines.
5. Links to information and tools of value to E. coli researchers.

EcoliHub is a growing system that will incorporate more resources and services as we grow. We are here to serve the user community. You can help us determine the direction of the EcoliHub project on our forum. You can also guide us to what is useful or desirable in future releases by completing our User Survey.

Please contact us at ecolihub@purdue.edu if you would like to join the EcoliHub community. EcoliHub is supported by the U.S. National Institutes of Health award U24 GM077905.

EcoliHub Databases

EcoliHub Databases are largely or wholly supported by the EcoliHub award, including:

EcoliLiterature is being developed as a comprehensive database of all articles, book chapters, and books with basic information on E. coli, its phages, and plasmids (EcoliHub Core Project).

EcoliPredict is a comprehensive database of computationally predicted and experimentally determined structures of proteins encoded by E. coli K-12 (Project Leader: Daisuke Kihara, Purdue).

EcoliWiki is being developed as a community annotation system for EcoliHub. The goal is to create community-based pages about E. coli K-12, its phages, plasmids, and mobile genetic elements for community annotation at Texas A&M University (Project Leader: James C. Hu, TAMU).

GenExpDB is a comprehensive database of publicly deposited E. coli gene expression data, which is hosted at the University of Oklahoma (Project Leader: Tyrrell Conway, OU ).

GenoBase is a E. coli database developed at the Nara Institute of Science and Technology (NAIST) in Japan that contains a wealth of information on comprehensive resources such as the Keio single-gene knockout collection, ASKA ORFeome clone set, and results from high-throughput and systematic experimentation. GenoBase is now being further developed at EcoliHub (Project Leader: Hirotada Mori, NAIST).

Participating Databases

Participating Databases actively collaborate with EcoliHub. While these database providers are independently supported, they may receive support from EcoliHub for specific joint projects.

EcoCyc is a professionally curated encyclopedic source of information on the genome, metabolic pathways, and regulatory network of E. coli K-12 at SRI international (Peter D. Karp, principal investigator (PI)).

EcoGene is a knowledgebase derived from extensive literature surveys and bioinformatics research that document the functions of DNA, protein and RNA in E. coli K-12 at the University of Miami (Kenneth E. Rudd, PI).

RegulonDB is the source of highly curated knowledge on regulation of transcription initiation, operon organization, and regulatory networks in E. coli at the University of Mexico, Cuernavaca (UNAM; Julio Collado-Vides, PI).

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