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PSB 2004
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The paper submission deadline has passed; notificaton of paper acceptance will be sent on September 8, 2003.
The ninth Pacific Symposium on Biocomputing (PSB) will be held January 6-10, 2004 at the Fairmont Orchid on
the Big Island of Hawaii. PSB brings together top researchers from
around the world to exchange research results and address open issues in all aspects of
computational biology. PSB provides a forum for the presentation of work in databases,
algorithms, interfaces, visualization, modeling and other computational methods, as
applied to biological problems, with emphasis on applications in data-rich areas of
molecular biology. PSB intends to attract a balanced combination of computer scientists
and biologists, presenting significant original research, demonstrating computer systems,
and facilitating formal and informal discussions on topics of importance to computational biology.
To provide focus for the very broad area of biological computing, PSB is organized into a series of specific sessions. Each session will involve both formal research presentations and open discussion groups. The 2004 PSB sessions are:
All papers must be submitted to russ.altman@stanford.edu in electronic format. The file formats we accept are: Adobe Acrobat (*.pdf), Microsoft Word documents (*.doc), and postscript (*.ps). Attached files should be named with the last name of the first author (e.g. altman.pdf, altman.doc, or altman.ps). Hardcopy submissions or unprocessed TEX or LATEX files will be rejected without review.
Each paper must be accompanied by a cover letter. The cover letter must state the following:
Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at http://www.smi.stanford.edu/projects/helix/psb-online/psb-submit/. If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.
Color pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission.
Contact Russ Altman (russ.altman@stanford.edu) for additional information about paper submission requirements.
Modeling in Systems Biology is often thought of as systems simulation, but in reality it can involve other forms of models and therefore requires a broader definition. Models may be numerically computable, but they also may be symbolical and accessible to inferential logic. Logical formalisms that describe complex phenomena are just as important as modeling molecular dynamics, and may lead to faster insight where the computational complexities are too great for a full-scale simulation
Contact:
All co-chairs
trey@wi.mit.edu, vs@genoscope.cns.fr, ENeumann@BeyondGenomics.com
This session will focus on methods in computational genomics that employ joint learning from multiple types of data. Preference will be given to methods that attempt to simultaneously discover patterns appearing in multiple data sources, rather than apply separate methods to each type of data. The performance of the methods should ideally be compared to the performance that can be obtained from learning from one data source at a time.
Contact: Alexander Hartemink
amink@cs.duke.edu
Alternative splicing is an essential yet complicated biological process, involving an estimated 30-60% of all human genes. Bolstered by genomic data and new experimental approaches, bioinformatics is emerging as an important tool for studying this phenomenon. For this first-time session, we are soliciting papers in three major areas:
Contact: All cochairs
hui_wang@affymetrix.com, leec@mbi.ucla.edu, yang@ym.edu.tw
The novel computational and statistical approaches required for planning, executing, and analyzing the data of large association studies aimed to elucidate the basis of complex-traits, either common disease, response to environmental impact, or adverse drug response. The goal of the session is the presentation and discussion of new research, methods, algorithms, and tools, that promise to facilitate the elucidation of the connections between genotypes and complex-traits using the data generated by high-throughput genotyping technologies.
Contact: All cochairs
delavefm@appliedbiosystems.com, kidd@biomed.med.yale.edu, A.R.Collins@soton.ac.uk
Ontologies provide an organizational framework of the concepts involved in biological processes in a system that can be used computationally for reasoning about biomedical knowledge. Ontologies provide a conceptualization of the domain that can be shared among diverse groups of researchers and computational systems. This session will explore the theories, techniques, and applications of biomedical ontologies. The overall session goal is to share new research ideas and achieve a better understanding of current approaches, issues, and challenges in ontology research.
Contact:
Olivier Bodenreider
olivier@nlm.nih.gov
+1 (301) 435-3246
The goal of structural genomics is to discover and characterize the three dimensional structure of all the proteins and other macromolecules found in nature. Presentations will focus on progress in solving the computational challenges in this field. Topic areas included in the discussions will be (1) Determination of all common scaffolds found in naturally evolved proteins, (2) Structure-based prediction and classification of function and (3) Elucidating structurally defined function.
Contact:
Sean Mooney
mooney@smi.stanford.edu
+1 (415) 370-5909