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New Alliances Prosper at ISMB 2002: Pathways, E. Coli Collaborations in the Works


Maybe the crummy weather in Edmonton last week was for the best: Apparently if you bring 1,500 bioinformaticists together in a sprawling conference center with few distractions for a week, they self-assemble into exciting new partnerships and collaborations. Among a number of research projects that had their beginnings at ISMB 2002, two large-scale alliances blossomed last week: the BioPathways Consortium initiated a community-wide project to improve the exchange of pathways-related information, and an international consortium of Escherichia coli cellular simulation projects was born.

The BioPathways project grew out of an open discussion chaired by Chris Sander of the Memorial Sloan-Kettering Cancer Center at the BioPathways SIG meeting August 1. The discussion centered around the feasibility of creating a large-scale open source pathway information resource, and meeting attendees weighed in on the various pros and cons of such a project. While most agreed that a public repository of pathway information would be a relevant and valuable resource, the technical details of integrating the disparate representations of metabolic, regulatory, signaling, and interaction data were acknowledged to be formidable.

As a first step, a working group was formed to develop an exchange format for pathway information with the initial target completion date of January 2003. The working group, which is composed of Sander, SRI’s Peter Karp, Chris Hogue of the Samuel Lunenfeld Research Institute, and several others, also hopes to develop a set of unique global identifiers for pathway-related objects, Sander said. Both Karp and Hogue said that techniques they have developed for their own pathway data resources — BioCyc and BIND, respectively — would be contributed to the project.

While the details of the working group’s activities and future plans are still under discussion, Sander noted that the goal of the group is “to increase the availability of pathway information in the public domain.”

Meanwhile, on the other side of the systems biology universe, a coalition of E. coli simulation projects took the first steps toward formally combining their efforts as well. At the Computer Modeling of Cellular Processes SIG meeting August 3, four national consortia of E. coli projects announced their intention to share data and resources with the eventual goal of a single, fully modeled E. coli cell. Masaru Tomita of E2Coli in Japan, Barry Wanner of EMC2 in the US, Mike Ellison of CyberCell in Canada, and Igor Goryanin of GlaxoSmithKline’s internal E. coli Whole Cell Model project represented the initial participants in the alliance, which plans to apply for an NIH “glue grant” in January 2003 to support the sharing of resources among E. coli projects already funded by the NIH. Wanner estimated that about 75 researchers would be involved in the project worldwide.

The aim of the alliance is to prevent redundancy in similar projects with the same general goals. However, the logistics of such an effort are not trivial. One issue on the table, for example, is whether the alliance participants should standardize on a particular strain of E. coli — a decision certain to have an impact on simulation projects already underway on different strains. Another issue — as always — is data sharing. Goryanin said that while he would like to make GSK’s data fully available to the public, he still has to “approach the legal people” at the company about the terms of release. Ellison noted that CyberCell also supports quick access to all data, but the scientific publication process often imposes a delay on the release of some types of biological information not covered by the “Bermuda rules” that ensure the immediate release of primary genomic data.

The alliance, whose official name is still under discussion, would be organized much like the Alliance for Cellular Signaling, which the NIGMS funded with a five-year, $25 million glue grant in 2000. Wanner estimated that a complete computational model of E. coli would require a total of around $100 million in funding and may be completed within a decade.

— BT

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