PSB '96 Technical Sessions

Minoru Kanehisa, Kyoto University.

Logical Simulation of Biomolecular Information Pathways

In addition to the catalogs and sequences of all genes and gene products being produced by genome projects, their functioning in a cell or in an individual organism is also being uncovered at an increasing rate owing to the advancement of molecular biology technologies. Once such functional data are properly computerized, it will become feasible to assist experiments, facilitate understanding, and even perform simulation, of information pathways controlling all aspects of living organisms. Here we present our efforts to organize functional data in such higher biological processes as the metabolic pathway and the cell cycle, and our attempts to perform logical simulations of these processes.

Dr. Kanehisa is the head of the Japanese Genome Informatics Research Project 1991-95 and the next Informatics Project 1996-2000. He received his D.Sci. from University of Tokyo in 1976, and did research on computational and theoretical molecular biology at Johns Hopkins University School of Medicine 1976-79, Los Alamos National Laboratory 1979-82, National Cancer Institute, NIH, 1982-85, Kyoto University 1985-present, and University of Tokyo 1991-95.

David Weininger, DAYLIGHT Chemical Information Systems.

CEX and the Single Chemist

CEX (Chemical EXchange) is an interface designed for chemical information exchange and interoperability in today's distributed environment. CEX provides a complete, working and extensible chemical information interface as commercial-quality, public domain software to which vendors can easily and freely port. CEX is an object-oriented mechanism for exchanging information in a semantically well-defined and program-independent manner which is particularly well suited for chemical information. CEX was developed by an alliance of chemical information software consumers, mainly large pharmaceutical companies with the assistance of software vendors, and is hardware operating system and vendor independent. CEX will be distributed and supported on Unix, Mac and PC/Windows platforms via a public FTP site (to be announced at PSB).

Dr. David Weininger is President of DAYLIGHT Chemical Information Systems, Inc. which produces tools used for doing chemistry as an information science including chemical databases, high-performance search engines, languages and an object-oriented chemistry toolkit. Dr. Weininger was trained at the Univerity of Rochester in Fine Arts, the University of Bristol in Chemistry and the University of Wisconsin in Water Chemistry. His research experience includes 4 years at the USEPA's National Water Quality Laboratory, Duluth, MN, 5 years at Pomona College, Claremont, CA, banjo player and a flight instructor. He currently heads DAYLIGHT's research office in Santa Fe, New Mexico.

Interactive Molecular Visualization

This track will highlight the various aspects of modern molecular graphics techniques and provide a forum for discussion of visionary ideas and challenging questions. We are also interested in providing the opportunity to present molecular problems which were solved using original visualization techniques.

The full call for papers is available, or email the session chairs micha@basel.sgi.com, henn@basel.sgi.com

Stochastic Models, Formal Systems and Algorithmic Discovery for Genome Informatics

This track is intended to cover stochastic models, grammars and formal systems for bio-sequences, and algorithmic discovery in biocomputing. More specifically, hidden Markov models and other types of stochastic grammars for the analysis, classification and structure modeling for the bio-sequences. It also concerns computational aspects of formal systems for bio-sequences, including formal lingusitics, splicing models and DNA computing.

The full call for papers is available, or email the session chairs at nitta@etl.go.jp

The Evolution of Biomolecular Structures and the Structure of Biomolecular Evolution.

All biological macromolecules have an evolutionary origin that is manifested in essentially every aspect of their biological and physico-chemical properties. In order to understand these macromolecules, it is necessary to understand the relationship between these properties and the evolutionary pressures that determined form and function. Information about the evolutionary history can be used to help predict the characteristics of these macromolecules. Conversely, these macromolecules encode this evolutionary heritage, and can provide insight into the process of molecular evolution.

The full call for papers is available, or email the session chairs at richardg@Chem.LSA.UMich.Edu, altman@camis.stanford.edu

Discovering, Learning, Analyzing and Predicting Protein Structure

This track will cover computational advances relevent to understanding and, ultimately, predicting protein structure and/or function, including stuctural classification at all levels, direct and "inverse folding", homology-derived, statistical, machine learning, analytic, modelling, pattern-based, and related methods.

The full call for papers is available, or email the session chairs at dunker@jaguar.csc.wsu.edu

Population Modelling

The minitrack on population modeling will sponsor papers on the application of high performance computing in understanding the dynamics of populations of plants and/or animals. Examples of topics include extinction models for endangered species, forest response models, "gap analysis" of fragemented ecosystems, population inventory analysis, and any other studies that use high performance computing and communication to study the interactions between species and their environment. We are interested in all aspects of high performance computing, including parallel algorithms, scientific visualization, and scientific databases.

The full call for papers is available, or email the session chairs at conery@cs.uoregon.edu

Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution

The use of the hybrid QM/MM potential in condensed phase simulations has only become possible very recently, thanks to advances in computer technology, statistical simulation methods, and quantum mechanical computational techniques. The hybrid QM/MM method has great potential in molecular modeling and in simulation to provide a consistent and an accurate description of intermolecular interactions in solution. To date, effort towards development of hybrid QM/MM methods has been largely centered on individual investigators and there has been a lack of meetings at which they can discuss problems specific to the area. The aim of the minitrack on hybrid quantum and classical mechanical methods at the PSB is to assess the state-of-the-art in the field and to highlight areas for future research by bringing together researchers who develop hybrid simulation algorithms and apply them to biological systems. We are accepting proposals for presentations of papers in any area that is relevant to the development or application of hybrid techniques to biological systems.

The full call for papers is available, or email the session chairs at mjfield@ibs.fr

Models of Control Systems in Biology

Excitation and suppression, up- and down-regulation, and on/off signal processing are systems that control a number of biological processes. These mechanisms control the signal processing systems in tumor growth, the immune system, gene expression, cardiovascular physiology, and muscle control. Optimal design for chemotherapy in cancer and optimal sampling schemes in pharmacokinetics, are variations on this theme. Mathematical models & appropriate theory, simulation, and statistical analysis of these kinds of dynamic systems will be discussed during this minitrack.

The full call for papers is available, or email the session chairs at Seth.Michelson@syntex.com

Computational Studies on the Design of Protease Inhibitors

Regulation of protease function has become a premiere strategy in combating human disease, due in part to the ubiquity of protease enzymes, but also because they are vulnerable to specific and selective inhibition by relatively small molecules. There has been an enormous increase in structural and activity data on proteases and their inhibitors over the past several years. Evaluation of similarities as well as divergence in these systems allows us to identify emerging trends and strategies. An increasing number of designed protease inhibitors are currently in clinical and preclinical development, so now is also a good time to assess the impact of computational approaches to studying these biological systems on the efficiency of the drug discovery process.

This minitrack will highlight the development and application of computational tools for the discovery of inhibitors of clinically relevant proteases within and across enzyme classes. Scientists who have made significant contributions to research on ligand-protease docking, dynamics simulations of ligand binding, the effects of entropy, solvation or long-range electrostatics on binding, prediction of binding modes and affinities, de novo design or related areas are encouraged to submit abstracts or full papers. Preference will be given to laboratories with experience in more than one class of protease target, since a major aim of the track is to compare and contrast strategies and structural features across classes.

The full call for papers is available, or email the session chairs at hodgecn@chemsci5.dmpc.com

Biocomputing Education: Challenges and Opportunities

This workshop will include a panel discussion consisting of several individuals that have developed and taught successful "biocomputing" courses. They will present ideas that work and don't work and offer sample curricula. Short demonstrations using the workstation projection system available of particularly successful techniqes will be an integral part. The openess of the forum will be encouraged and audience participation will be critical. We are also soliciting research papers and poster abstracts on biocomputing education.

We are also pursuing ideas for a biocomputing education web resource. Briefly, we would like to have everybody that has expressed any interest in participating in the Education Workshop create web page(s) covering their course offerings.

The full call for participation is available, or email the session chair at thompson@jaguar.csc.wsu.edu

Internet Tools for Computational Biology

This workshop will explore access to biological computational resources via electronic networks. Computational tools play a more important role than ever in biology, and the internet makes these tools available to researchers and students world-wide. Electronic Mail servers have been in used for very long time already in order to access very large archives of molecular biology data, such as the sequence data providers. The expansion of campus information systems (e.g. GOPHER) allowed to implement immediate, interactive access to resources in both query and retrieval. More recently, the burst of World Wide Web has accomplished to make data accessible on networks which have never been visible in this kind of presentation before. The workshop invites contributions by researchers and practitioners addressing these topics.

This workshop has its own home page, or email the session chair at doelz@ubaclu.unibas.ch

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