This session is intended to be a forum for addressing the advances and needs of computational tools for modeling and managing genomic, pathway and interaction information, including metabolic pathways, signal-transduction pathways, genetic regulatory circuits, protein-protein interactions, and other types of biological interactions. A key interest is how to relate a system-theoretic point-of-view with our current gene/protein-centric approaches, and what kinds of applications are possible with such models.
Genomics has revolutionized biomedical research with the ongoing determination of the nucleic-acid sequences of many organisms. However, such information is not an end in itself but the foundation to understanding the biological characteristics of an organism, that is, inferring its phenotype. The characterization of an organism is largely based on a thorough knowledge of its metabolic machinery, and the management of both genomic and metabolic information is not a trivial matter. Developments in Bioinformatics have helped improve data manipulation in both areas and are helping bridge the gap between genomic and metabolic data.
On one hand, computational analysis of biological pathways have been
evolving in the past years due to the contributions from many disciplines,
including biochemistry, chemical engineering, developmental biology, artificial
intelligence, simulation, and control theory. An area of particular
interest here is the development of new techniques for the elucidation
of protein-protein interaction pathways. Conversely, genomic research
is producing an ever growing amount of data that is being studied through
sequence-analysis computational techniques in order to extract product,
regulation and evolutionary information. These areas of Bioinformatics
research, both by themselves and in synergetic combination, are going to
provide the basis for a more complete understanding of the biology of specific
organism, with the corresponding applications on areas that go from bacterial
culturing to drug discovery.
Issues relevant to this session include:
In short, the session will address the issues of modeling, data
representation, simulation and integration/display of multiple kinds of
biological data in the genomic/metabolic domain.
Scientists who wish to participate in the session, but who do not wish
to submit a full paper, are welcome to submit a two page abstract, which
will be distributed at the meeting separately from the archival proceedings.
All participants are welcome to display posters and give live computer
demonstrations.
All PSB paper submissions must be submitted electronically via email
to Russ Altman (altman@smi.stanford.edu)
on or before July 17, 2000.
We accept postscript, pdf and Microsoft Word format files. We can NOT accept Tex files or other word processors. Please follow the paper formatting instructions available at:
ftp://ftp-smi.stanford.edu/pub/altman/psb.
Please note that all submissions must be accompanied by an (email) cover
letter that specifies by which specific session (if any) the paper should
be reviewed. Please also include a statement in the cover letter
that the paper that contains original unpublished results not currently
under consideration elsewhere and that all co-authors concur with its contents.
Eric Neumann
3rd Millennium, Inc.
eneumann@3rdmill.com
Pedro Romero
Artificial Intelligence Center, SRI International.
promero@ai.sri.com