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Microbial Metabolism

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This workshop took place at eSI April 6th -8th 2011. The lead organiser was Jamie Wood. The workshop involved 17 participants, including international participants from University of Illinois (US), Broad institute (US), Chalmers (Swi), INRIA (France) and CNRS Marseille (France). All invitees gave talks followed by a roundtable discussion. Many of the speakers at this meeting hold senior positions on biochemical and electronic standards panels; this meeting provided an unusual chance to discuss important community-wide issues of standardization and policy in an informal context.

Key ideas emerging from this workshop included

There are immense possibilities now open to metabolic modelling as it is the only whole-organism modelling framework within systems biology. This is both in terms of breadth – the number of organisms with whole or partial metabolic reconstructions is increasing fast and there is much greater coverage across different genera – and in terms of detail – metabolic modelling looks like a tempting candidate as a framework for whole organism genotype to phenotype kinetic modelling.

The lack of input from the mathematical sciences needs addressing urgently. Systematic understanding of optimisation methodology beyond linear flux balance analysis (FBA) in the context of metabolism is required for the field to be better rounded. In particular, identification of relevant objective functions need to have both biological and mathematical justification.

The importance of e-Science in past, present and future development. This broad area is hugely dependent of the quality and quantity of community maintained databases such as BiGG, Kegg and organism specific Cyc database such as EcoCyc. Standards of representation and ontology are critical in maintaining the usefulness of these resources as well as the need to make the quality of the stored data more uniform.

The field needs to become more visible. The information on how to perform many of the essential steps in creating a model that will function in FBA needs to become more public and transparent. The immense future potential of the field also need to be better communicated to other scientists and non-scientists through training and dissemination events.

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