Pacific Symposium on Biocomputing 11:v-vii(2006)

PACIFIC SYMPOSIUM ON BIOCOMPUTING 2006
The stunning advances in stem cell research by Drs. Woo Suk Hwang and Shin Yong Moon of the Seoul National University have captured the world's attention. Meanwhile, stem cell research in the U.S. is being impeded for a complex of reasons. Bioethicist Eric Meslin, Director of the Indiana University Center for Bioethics and the Assistant Dean for Bioethics of the Indiana University School of Medicine, will address this timely issue in his keynote lecture. We are looking forward to this extremely important presentation and the discussion to follow, not only for the insight it will provide on this particular issue, but also for illuminating trends in the development of U.S. science policy over the last several years. Michael Ashburner, Professor of Biology at the University of Cambridge and former Joint-Head of the European Bioinformatics Institute (EBI), will deliver the second keynote lecture. His presentation will describe the use of ontologies in biological research. The importance of ontologies for all of our research has been reflected in past sessions on this topic at PSB. The 13t h International Congress on Genes, Gene Families, and Isozymes was h e l d in Shanghai, China, from September 17-21, 2005 (http://www.cafs.ac.cn/page/cafs/guanggao/jiyin/show.asp). This meeting is but one of many international meetings that are being held with increasing frequency in Asia. The significant increases in investment in research as evidenced by the stem cell advances, the improved overall scientific infrastructure as evidenced by the international meetings, and the general increases in the quality of life are encouraging significant numbers of Western-trained Asian scientists, including many PSB participants, to consider accepting research positions in the Far East. We anticipate that these trends will lead to increasing numbers of PSB participants from Pacific Rim countries in the coming years. Such a result would be entirely consistent with the long range goals of the PSB organizers. Thanks to the effort of Jie Sun and Tiffany Murray of Indiana and Stanford Universities, respectively, PSB articles are now linked with PubMed. Next time your PubMed query leads to a PSB article, our logo ( ) will appear above the article's abstract, which of course provides a direct link to the article itself. If you haven't discovered this already, we invite you to try it out. So far only PDF versions of the articles are available. This effort was no small task. The various electronic forms of many different PSB articles had to be converted one-by-one into PDF format and then checked for fidelity. In the early years, PSB articles were submitted on paper, and in many instances the authors never followed up with electronic versions of their published articles. In still other cases, the electronically formatted articles exhibited differences from the actual articles in the PSB proceedings. In all such cases, the paper versions were scanned electronically and PDF-formatted manuscripts were created from the scans. Thus, except for the session introductions and the prefaces to each


year's book, the articles in PSB can now be reached automatically from PubMed. We believe that this will be a significant gain for all of you who have published with us or who use articles from PSB in your research. Cudos to Jie Sun and Tiffany Murray for carrying out this project. The PSB online proceedings web site has also introduced a Google-style search facility which makes it much easier to find articles based on simple word searches. At each PSB meeting, the seeds for the following PSB are planted as participants begin to think about possible sessions for the next meeting. Over the years by discussions with the various participants, each of the organizers has helped to nurture ideas into session proposals. We would like to call to your attention that the process of organizing a session is a great way for a young faculty member to gain visibility for her- or himself, and just as important, this is a great way to stimulate interest in and focus on newly emerging areas of study. We are proud that many areas in biocomputing received their first significant focused attention at PSB. It is no coincidence that many of these sessions were conceived and executed by some of our younger participants. If you have an idea for a new session, we the organizers are available to talk with you, either at the meeting or later by e-mail. Again, the diligence and efforts of a dedicated group of researchers has led to an outstanding set of sessions. This year, in addition to the sessions, there will also be survey tutorials. These tutorials of one hour for each session are intended to provide key background information for the upcoming presentations. These organizers and their sessions are as follows: Bobbie-Jo Webb-Robertson, Bill Cannon, Joshua Adkins, and Deborah G r a c i o, Computational Proteomics Andrew G. Clark, Andrew Collins, Francisco M. De La Vega, Kenneth K. Kidd, Design and Analysis of Genetic Studies After the HapMap Project Kevin Bretonnel Cohen, Olivier Bodenreider, and Lynette Hirschman, Linking Biomedical Information Through Text Mining Maricel Kann, Yanay Ofran, Marco Punta, and Predrag Radivojac, Protein Interactions in Disease Robert Stevens, Olivier Bodenreider, and Yves A. Lussier, Sematic Webs for Life Sciences In addition to the sessions and survey tutorials, this year's program will include two in depth tutorials of three hours each. The presenters and titles of these tutorials are as follows:


Giselle M. Knudsen, Reza A. Ghiladi, and D. Rey Banatao, Integration Between Experimental and Computational Biology for Studying Protein Function Jotun Hein, Mikkel Schierup, and Thomas Mailund, Association Mapping: Fundamental Principles and Applications The Department of Energy and the National Institutes of Health are thanked again for their continuing support of this meeting. Their support both enables the infrastructure of the meeting and also provides travel grants to many of the p a r t i c i p a n t s . Applied Biosystems and the International Society for Computational Biology continue to sponsor PSB, and as a result, we are able to provide travel grants to many meeting participants. P S B is now receiving far more submitted manuscripts than can be accommodated in our program. As a result, many excellent papers cannot be included, and as a further result, the task of reviewing the papers has become increasingly difficult. Thus, we would like to especially acknowledge the many busy researchers who found the time to review the submitted manuscripts on a very tight schedule. The partial list following this preface does not include many who wished to remain anonymous, and of course we apologize to any who may have been left out by mistake. Aloha! Pacific Symposium on Biocomputing Co-Chairs September 27, 2005 Russ B. Altman Department of Genetics, Stanford University A. Keith Dunker Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Lawrence Hunter Department of Pharmacology, University of Colorado Health Sciences Center Teri E. Klein Department of Genetics, Stanford University