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Led by Lion, EU Consortium Seeks to Build a Sustainable Bioinformatics Framework

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A private/public consortium led by Lion Biosciences is proposing a “new business model” for building — and sustaining — a European network of bioinformatics software and databases.

In mid-November, the 19-member consortium, called CONDALIS (Consortium to Provide Sustainable Exploitation of Life Science Data), submitted a proposal to the European Union’s Sixth Framework Program to create a “virtual system” that will link bioinformatics data and software across European research organizations. While the EU won’t fund the proposal until May — if it approves it at all — that hasn’t prevented the CONDALIS participants from jumping into the project with both feet.

Clemens Suter-Crazzolara, a head of business development at Lion and CONDALIS coordinator, said that several EMBnet nodes participating in the project have already “started working on the technical implementation of the system,” and that a prototype of the framework should be available by February.

Lion’s SRS data-integration system, which will serve as the technical foundation for the CONDALIS framework, is already installed at EMBnet nodes and “hundreds” of other research organizations across Europe, Suter-Crazzolara said, giving the project participants a head start in linking their resources. However, he noted, SRS servers at different sites are currently out of synch — with different software, databases, or even different versions of the same resources — so users who want to access all the available data have to visit several different sites via multiple queries.

CONDALIS will use the new web services capability in SRS 8 to “create clients that virtually link all these services together,” Suter-Crazzolara said. “That means that if you have a query, you only have to go to one server, and that server will pick up all the data from all the different servers located in Europe or even worldwide.” He said that the system will include a number of access-control features to ensure security for commercial users.

The February prototype will include six SRS servers and a “limited” number of databases, Suter-Crazzolara said. “They will all have the same versions of tools and databases, and the user can then go to one of the servers, launch a query, and will not see where his query results come from — he will simply get the result that he asked for.”

But Suter-Crazzolara said that the technical implementation of the system is only one of three primary components in the CONDALIS proposal. In addition to the technical platform, he said, the project will emphasize systems biology research as the ultimate use case for the seamless integration of multiple sources of complex biological data.

Two CONDALIS partners — the Free University of Amsterdam and the Max Plank Institute for Molecular Genetics — will contribute their biosimulation and modeling software to the project to determine whether the framework “really answers the question that somebody involved in systems biology would have,” he said.

The third aspect of the project will address a persistent problem for bioinformatics resources: long-term financial survival. “There are many public efforts in bioinformatics, but they all have the same problem,” Suter-Crazzolara said, “and that is that after government funding stops after a certain period, they have difficulty sustaining [themselves] into the future.”

Noting that commercial bioinformatics efforts have had their financial troubles, too, Suter-Crazzolara said that the goal of the consortium is to secure EU funding to “jumpstart” its initial efforts, “and after that, we would like to have perhaps a user license fee, which is then used by the consortium itself to ensure that it can continue beyond the funding period.”

He stressed that the details of the proposed commercial model are still under discussion, however. “We have different ideas that we’re playing with at the moment,” he said. “It’s too early to tell exactly what kind of model we will choose, but sustainability is something that is very high on our agenda.”

Suter-Crazzolara declined to disclose the amount of funding that the CONDALIS partners requested. The proposal was submitted as part of the FP6’s third call for research proposals in life sciences, genomics, and biotechnology, which has a total budget of €540 million ($718 million). The four-year FP6 program has a total budget of €17.5 billion, with €2.3 billion earmarked for life sciences research.

In the face of declining revenues over the past several years, tapping into public funds to support internal R&D may seem to be a no-brainer for companies like Lion, but Suter-Crazzolara said the company carefully weighs the pros and cons of such projects before submitting proposals. “It is in many cases a good opportunity to invest in manpower,” he said, but, “on the other hand, some of the projects … have a large administrative overhead. And that is what we have seen with some projects in the past, where the effort from Lion has been very big, but what comes out does not represent the same worth.”

The CONDALIS proposal “fits very well with the company’s strategy, both from a technological as well as from a business view,” he said.

Lion is also working on two other FP6-funded projects that will use SRS as a technical foundation: EMI-CD (European Modeling Initiative Combating Complex Diseases), a project to develop a publicly available software platform for molecular modeling; and SIMDAT, a project to develop grid computing technology for product development and production process design [BioInform 10-18-04]. Suter-Crazzolara said the company would consider participating in additional publicly funded projects — both in Europe and elsewhere — as long as they fit with Lion’s strategy.

In addition, he said the CONDALIS network is expected to expand worldwide, with several sites in South America already expressing interest in participating. As for US involvement, “there are several public institutes that have SRS servers already, and we want to start discussions with them.”

Although the funding for the project is not guaranteed, Suter-Crazzolara said that Lion intends to continue supporting the effort as part of its own development roadmap. “Web services technology is extremely powerful to bring that information to the end user, and for Lion, for our business, it’s very important to move in that direction.”

While Lion and its partners are not waiting for a check from the EU to begin implementing the project, “the funding will help us tremendously to speed up that whole process,” Suter-Crazzolara said, “but we are working on it already.”

Additional information on CONDALIS is available at http://www.condalis.org, and information on the SRS federation prototype project is at http://www.srsfed.org.

— BT

 

CONDALIS Participants

  • Biobase
  • EMBL, Heidelberg
  • Free University of Amsterdam
  • Free University of Brussels
  • HealthGrid
  • Imperial College London
  • Infobiogen (Evry, France)
  • Laboratory of Corpuscular Physics, France
  • Lion Biosciences
  • Max Planck Institute for Molecular Genetics, Berlin
  • Oracle
  • Polish Academy of Science, Warsaw
  • The Fraunhofer Institute for Algorithms and Scientific Computing
  • The German Cancer Research Institute, Heidelberg
  • The Institute of Biomedical Technology (Bari, Italy
  • The Institute of Molecular Biology (Bratislava, Slovakia)
  • The Linnaeus Center for Bioinformatics (Uppsala, Sweden)
  • Universitat Jaume I, Spain
  • University of Twente, the Netherlands

 

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