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Practical Tools For Innovation
O'Reilly Bioinformatics Technology Conference
January 28-31, 2002 -- Tucson, AZ
Chambered Nautilus

Speakers

O'Reilly & Associates specializes in translating the innovator's knowledge into useful skills and The O'Reilly Bioinformatics Technology Conference is designed to deliver these skills to you.

Our speakers innovate; in one-way or another, all have blazed new trails in bioinformatics. In line with our emphasis on technology, our speakers refrain from marketing oriented hyperbole. They focus on the hard core, the important challenges and discoveries presented by the brightest minds in the trenches of bioinformatics. They will give you immediately useful knowledge - skills you can take back to improve the way you do research.


Keith Allen, Ph.D.
Keith Allen is a Bioinformatics Scientist at Paradigm Genetics. He received his BA in Biology from Reed College in 1983 and his PhD in Molecular Biology from the University of Colorado, Boulder in 1991.

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Dan Appelman
Dan Appelman is a partner at the law firm Heller Ehrman White & McAuliffe where he is co-chair of the firm’s Information Technologies National Practice Group. Dan’s practice emphasizes the protection and commercial exploitation of proprietary rights in high technology products and services, particularly in the computer hardware, software, telecommunications and Internet areas. He has represented clients in licensing transactions in the United States and abroad and in establishing copyrights, trade secret rights and trademark rights related to their inventions. Dan has represented many companies that develop bioinformatics-related technology. Dan also represents the Open Bioinformatics Foundation.

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R. Geoffrey Avery
R. Geoffrey Avery is a computer scientist at GlaxoSmithKline where he builds tools for bioinformaticians. He is also a Perl Monger and occasional contributor to CPAN.

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Malay Kumar Basu
Malay Kumar Basu has M.Sc. degree in Zoology and M.Tech degree in Biotechnology. Currently, He is a graduate student in Molecular Biology in Centre for Cellular and Molecular biology, India where he is trying to give finishing touches to his thesis on “The cold adaptation in Antarctic bacteria”. He is an autodidact, likes to play around with computers in his spare time and started his bioinformatics work around a year back.

His first project, on an interface for bioinformatics services on web called “SeWeR”, was a success as judged by the popularity which bolstered his confidence to more ambitious work in computational geometry. This led to the creation of “Pastel”, a library in Perl to generate Scalable Vector Graphics (SVG). He wrote Pastel to act as a base to write “BioSVG”, a set of Perl modules to generate SVG for biological data. As a prototype he wrote “Savvy” to draw plasmid map in SVG using BioSVG and currently he is working to finish Pastel and BioSVG.

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Doron Betel
Doron betel is a graduate student in Dr. Chris Hogue's Bioinformatics Lab at the Mt. Sinai Hospital Research Institute in Toronto. In his early Bioinformatics days Doron has developed a pattern matching program for biological sequence using NCBI C programming toolkit. Currently Doron is building a Flash graphic visual tool for viewing biological pathways in BIND using NCBI C++ toolkit and working on protein interaction discovery work.

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Ewan Birney
Ewan Birney has a PhD in Genetics and is a long time open source bioinformatics programmer. He is the PI (principle investigator) for a group of 15 people researchers in genome informatics, with a particular focus on the human genome.

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J. W. Bizzaro
Jeff Bizzaro is the founder and president of Bioinformatics.Org. He is a Ph.D. student in biochemistry at the University of Massachusetts in Lowell, and his interests include structural and evolutionary bioinformatics, data visualization, user interfaces, and advocating freedom and openness in science. He holds an M.Sc. in biochemistry from Boston College.

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Steven Brenner
Steven E. Brenner is an Assistant Professor and leader of a computational genomics research group at the University of California, Berkeley. His research interests include computational approaches for structural genomics and sequence analysis, and the use of both of these to infer molecular function. Brenner was educated and trained at Harvard, the MRC Laboratory of Molecular Biology and Cambridge University, and Stanford. He is best known in the open source community for authoring cgi-lib and for his role as founding coordinator of the bioperl effort. He is a past director of the International Society for Computational Biology and is a founding director of the Open Bioinformatics Foundation.

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Roger Brent
Born Spartanburg, South Carolina, 1955. BA Computer Science and Mathematics, 1973, University of Southern Mississippi, where he did some work attempting to apply AI techniques to protein folding. Ph.D., Harvard University, 1982, Biochemistry and Molecular Biology, for studies with Mark Ptashne. As a graduate student, he showed that the E. coli lexA gene repressed genes involved in the response to radiation damage, cloned the gene, produced and purified its protein product using and in some cases extending the newly developed recombinant DNA methods, and studied binding of the repressor to its operators, showing that its differential binding affinity for these sites affected the timing of the response. As a postdoctoral fellow, also with Mark Ptashne, he tested a number of ideas about the mechanism of transcription regulation in yeast by using the prokaryotic LexA protein and in subsequent experiments creating chimeric proteins that carried LexA fused to activators native to yeast. These "domain swap" experiments established the modular nature of eukaryotic transcription regulators. As a professor at Massachusetts General Hospital and Harvard Medical School (Genetics, starting 1985), Brent and coworkers used yeast transcription that depended on chimeric DNA bound proteins as a genetic probe for protein function in higher organisms. This work led to the development of working two-hybrid methods (1988-1993), to the ability to scale them up via interaction mating (1992-1994), and to the eventual development of protein interaction methods into broad but shallow way to learn more about biological function. In parallel (1993-2001), Brent and coworkers developed peptide aptamers as reverse "genetic" agents to study the function of proteins and allelic protein variants, and, more recently, as dominant forward "genetic" reagents to identify genes and pathway linkages in organisms, such as human cells, that are intractable to classical genetic analysis. Perhaps as important as the actual technologies is the coeval development by Brent and coworkers of ideology (e.g. doctrine) for using them. This work is described in about 80 research papers and reviews. In parallel to his academic work, Brent is a longtime (since 1984) advisor to the biotech and pharma industries. He serves on the SAB of American Home Products (GI/WAR), chairs scientific advisory boards for several smaller companies, and does significant ad hoc consulting work in genomics and computational biology. He is one of the founders (1987-2001) of Current Protocols, including Current Protocols in Molecular Biology, a "how to clone it" manual, which is updated every three months and has about 10,000 subscribing labs, and he is founder and organizer (since 1994) of the "After The Genome" workshops. He is an inventor on 10 issued and several pending US Patents. Since the middle 1990s, he has exhorted and advised various bodies in the US and abroad on functional genomics and computational biology, including in particular the NIH, the Wellcome Trust, the NSF, DARPA, and other parts of the US Defense Department. In 1998, Brent started, with Sydney Brenner, The Molecular Sciences Institute in Berkeley, California. TMSI (www.molsci.org) is a non-profit research institute. Its mission is to create a predictive biology by weaving together functional genomic and other experimental information and using that knowledge to develop predictive simulations of biological function. If successful, work at the Institute will increase biological understanding and may bring about new models for human therapy. It may also shed light on how living systems process information and contribute to the rise of a design based engineering of biological systems. In late 2000, Brent joined the faculty at UCSF as an adjunct professor and became Director of the Institute. In 2001, he was named CEO, President, and Chair of the Institute Board of Trustees.

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Travis Brown
As a technology manager in Apple's Worldwide Developer Relations group, Travis Brown helps developers leverage the technology portfolio of Mac OS X to create innovative applications for the platform. Brown focuses on graphics and imaging related issues and handles technologies such as Quartz, ColorSync, Image Capture, printing, and PDF. He has been involved in the field of computer graphics and digital imaging for the last decade.

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Shane Caraveo
Shane Caraveo is a senior developer at ActiveState, where he is the technical lead for the Komodo IDE, a multi-language IDE for scripting languages that is developed on top of Mozilla. He has four years experience developing on Mozilla using XUL, XBL, Javascript, and Python. He is a core PHP developer, working extensively on SOAP, FastCGI, and the Windows port. He also co-authored the DBGP protocol for providing a standardized debugger communication layer in scripting languages.

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Jesus Castagnetto
Jesus Castagnetto, a physical-organic chemist by training and a computational chemist and net-head by inclination, works in The Scripps Research Institute’s Metalloprotein Structure and Design Group. He developed the Metalloprotein Database and Browser (MDB), a bioinformatics resource with both a user interface and a set of APIs (web services).

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Michael Caudy, Ph.D.
Michael Caudy received a Ph.D. in Biophysics from U.C. Berkeley and postdoctoral training at U.C. San Francisco. He was at Cornell University Medical College from 1990 to 1999, studying the cellular, molecular and genetic mechanisms that control neuronal development. In 1999 he moved to Burke Medical Research Institute, an affiliate of Cornell.

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Tim Clark
Speaker biography coming soon.

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Judith Cohn
Judith Cohn is a senior member of the bioinformatics team at the Center for Human Genome Studies at Los Alamos National Laboratory, where her primary focus is the design, development and maintenance of distributed applications for tracking, analyzing and planning how to generate genomic sequencing data. Judith is unusual in that she holds a PhD in molecular biology but has worked for the last 15 years as a software engineer in both academia and the private sector.

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Damian Conway
Damian has been a vi addict for quarter of a century. His h, j, k, and l keys are polished blank with overuse. He's noremapped his space and tab keys to more useful functions. His .vimrc is over 600 lines long, about 90% of it scripting code. VIM is his second favorite programming language and his only IDE.

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Chris Dagdigian
As a founding partner of the independent consulting firm BioTeam Inc., Dagdigian specializes in research computing and infrastructure technology issues in the life sciences. A supporter of free software and open standards for life science research he is a founding member of the Bioperl Project, co-founder of the Bioclusters mailing list, and serves on the board of directors as Treasurer of the Open Bioinformatics Foundation.

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Andrew Dalke
Andrew Dalke is the founder of Dalke Scientific Software, LLC, which provides commercial quality software products and services that help bioinformaticians and chemists do more science in less time. He has a background in both structural biophysics and computer science and has been developing software tools for the computational life sciences for nearly ten years. His emphasis is in developing usable large-scale software systems for this field, based on a user-centered design and good software engineering practices.

A supporter of free software and open standards for life science research he is a cofounder of the Biopython (www.biopython.org) and serves on the board of directors for the Open Bioinformatics Foundation (www.open-bio.org). Andrew has been developing in Python since 1998 but actually started participating in the Python Software Activity and conferences in 1997, based on the reading the documentation.

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Warren L. DeLano
By day, Dr. Warren L. DeLano is an informatics scientist for Sunesis Pharmaceuticals. By night, Warren is an open-source software developer. His lead project, PyMOL, is the most powerful molecular graphics package currently available as completely unrestricted open-source software. It is also one of very few high-performance molecular graphics packages to support a native Python API.

DeLano's mission is to develop high-impact biopharmaceutical software. As a student and scientific programmer at Yale University, he was a developer of the popular X-PLOR and CNS programs for structural biology. DeLano obtained his Ph.D. in Biophysics from the University of California, San Francisco in 1999. He performed the bulk of his graduate research at Genentech, Inc. under the supervision of Dr. Jim Wells. DeLano used phage display, X-ray crystallography, and computational tools to study the origins of binding energy in protein interfaces. He developed the RigiMOL program to analyze conformational changes in protein interfaces, and SiteFinder to study properties of protein surfaces.

In 1998, DeLano left Genentech to help Jim Wells launch Sunesis Pharmaceuticals, Inc. a company focused on exploiting energetic "hot spots" on proteins for purposes of drug-discovery. Over the past three years, DeLano has led the development of informatics and IT infrastructure at Sunesis, where open-source components played a major role, from deployment of Linux servers and a Linux computing cluster, to creation of a Python-based chemical informatics platform. DeLano believes that the pharmaceutical industry has a tremendous but largely unrealized interest in supporting open-source software development.

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Michael Deyholos
Mike Deyholos earned a Ph.D. in molecular biology from McGill University in Montreal, and now works at the University of Arizona in Tucson, where he produces and analyzes microarrays to learn how plants cope with drought. Almost two years ago he swore, Scarlett O'Hara style, that he would never again do multiple BLAST searches via the web, and he sat down to learn the requisite computer skills. Since then he has established several microarray databases built exclusively on Open Source tools, and continues to try to make these databases more useful so that people will get off his back.

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Karl T. Diedrich
Karl Diedrich received his Master of Microbiology, Molecular Biology Biochemistry, at the University of Idaho in 2000, and his DEODAS: Degenerate Oligonucleotide Design and Analysis System Bachelor of Biology, from Eastern Washington University, 1993.

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Christopher Dwan
Christopher Dwan is a bioinformatics programmer at the University of Minnesota's Center for Computational Genomics and Bioinformatics. He helps life scientists apply high-performance computational resources to their research.

How did Dwan get into bioinformatics? “I have always been fascinated by the mechanisms of life. Many members of my nuclear family are physicians. I've always wanted to explore biochemistry and ‘how life works,’ but my aptitudes are stronger for computers than with people. My prior work was in vision processing and pattern recognition. One of my colleagues had taken his Ph.D. in biochemistry, and we would frequently talk about the potential for applying machine learning and information sciences to biological problems. I would also chat with my family about how their research/work might be a bit more productive if we could combine our disciplines. Thus, when the opportunity came for me to work with a bioinformatics and genomics research group, I jumped at it.”

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Sean Fagan
As a Software Customer Seeding Engineer in Apple's Worldwide Developer Relations group, Sean Fagan is responsible for helping developers transition from other UNIX (and UNIX-like) systems to Mac OS X. Fagan is long-time UNIX and Open Source developer and, prior to joining Apple in 2001, he worked at such companies as Cygnus Support, The Santa Cruz Operation, Inc., and Stratus Computer.

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Howard Feldman
Howard is a Ph.D. candidate in the lab of Dr. Christopher Hogue, at the Samuel Lunenfeld Research Institute, Mount Sinai Hospital in Toronto, Canada.

He has previously completed a B.A.Sc. in Biomedical Engineering at University of Toronto and has been programming computers since he was just out of diapers.

Howard is currently working on an algorithm to help solve the protein folding problem.

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Linnea Fletcher, Ph.D.
Dr. Linnea Fletcher is the Biotechnology Program Coordinator at Austin Community College, and the South Central Regional Director for the NSF-funded, Advance Technology Education, Biotechnology Center grant, Bio-Link. The overall goal of the grant is to promote biotechnology and bioinformatic education, focusing on biotechnician training. For the past two years she has worked with other educators to develop modules in the field of bioinformatics and train both secondary and postsecondary educators in this rapidly, emerging field.

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Nigel Fletcher-Jones
Nigel Fletcher-Jones is Senior Vice President of Nature America Inc, New York and Publisher of the Nature research journals, including Nature Genetics, Nature Biotechnology and Nature Medicine, and was formerly Vice President of Cell Press, publishers of Cell and Molecular Cell. He has a long-standing interest in the integration of high quality scientific content and bioinformatics on the Web and in the development of community-focused publishing.

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Matthew Frome
Speaker biography coming soon.

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Damian Gessler
Dr. Gessler's expertise is in theoretical evolution and population genetics as studied via computational techniques. He has 19 yrs experience in computer programming and systems operations. After his Ph.D. in theoretical population genetics, Dr. Gessler wrote statistical algorithms to map quantitative trait loci in outbred populations. Recently, he has been the Science Lead on NCGR's Integrated System ISYS.

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Cynthia Gibas
Cynthia Gibas recently joined the faculty at Virginia Tech from from the National Center for Supercomputing Applications. She is building research programs which feature open source development efforts.

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Brian Gilman
Speaker biography coming soon.

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William Gleason
Bill Gleason does research and teaches in the Department of Laboratory Medicine & Pathology at the University of Minnesota Medical School. He is also a fellow of the Minnesota Supercomputer Institute. One current research interest is the use of parallel computing, especially on Linux clusters, for practical applications in computational biology and medicine. Bill was co-developer of an early protein analysis package (PAP) and continues to take a "tools approach" in his research related to biological structure.

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Ben Goertzel
Ben Goertzel, Ph.D., is CEO of the start-up Cognitive Bioscience, a firm focused on analyzing biodata with advanced AI. From 1998-2000 he was CTO/founder of Webmind, an AI software company. From 1989-97 he held professorships in mathematics, computer science and psychology. He has authored 6 books and many research papers.

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Martin Gollery
Martin Gollery is the Associate Director of Bioinformatics at the University of Nevada at Reno, the Chief Scientific Officer of Infoceutics, and the CEO of Tahoe Informatics. He has been the Director of Research at TimeLogic, a high school science teacher, an aerospace engineer, a photographer, and a wedding singer.

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Suzanne Grindle
Speaker biography coming soon.

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Tania Broveak Hide
Speaker biography coming soon.

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Uwe Hilgert, Ph.D.
Dr. Uwe Hilgert is a microbiologist with many years of experience in college and pre-college science education. He is a fellow of the prestigious Alexander-von-Humboldt Foundation and the National Institute for Science Education, and works currently as science educator, web designer, and curriculum developer for the Dolan DNA Learning Center at Cold Spring Harbor Laboratory.. He has taught molecular biology to senior citizens, and developed cgi-based appointment calendars and web-based, interactive advising tools for biology Freshman. Recently, he developed Bioinformatics in the Classroom, a course for high school teachers and community college faculty. During his presentation he will discuss the teaching of bioinformatics and advanced biology at the high school level, and the support of pre-college education by bioinformatics, genomics, and proteomics professionals.

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Christopher Hogue, Ph.D.
Christopher Hogue brings a diverse research background to his role as Senior Scientist at the Samuel Lunenfeld Research Institute of Mt. Sinai Hospital, Toronto, Ontario. Hogue earned his Bachelor of Science degree from the University of Windsor and his Doctor of Philosophy from the University of Ottawa, both located in Ontario, Canada. Chris worked as a postdoctoral researcher at the U.S. National Institutes of Health in the National Centre for Biotechnology Information where the sequence database "GenBank" is maintained and distributed. At NCBI Chris helped develop a new 3-Dimensional structure database and wrote a widely used program for visualizing biological molecules called "See-in 3-D".

Chris's research team developed the Biomolecular Interaction Network Database and also study protein folding using Beowulf clusters and distributed computing. He is an Assistant Professor of biochemistry at the University of Toronto, where he teaches in various bioinformatics courses as well as courses in proteomics and protein structure and function. Chris is also one of the founders of the Candadian Bioinformatics Workshop series (www.bioinformatics.ca) and is engaged in the training of hundreds of new bioinformatics professionals. Well known and well respected in the biochemistry field, Hogue has authored and co-authored over 30 papers, and several book chapters on both biochemistry and bioinformatics. He has also given over 50 presentations and holds six patents in the biomolecular field. Furthermore, Hogue has received several major grants for his research, including a NCBI Genbank Fellowship, and was named a Canada Foundation For Innovation Researcher, while at the Samuel Lunenfeld Research Institute.

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Leroy Hood, Ph.D.
Dr. Leroy Hood is recognized as one of the world’s leading scientists in molecular biotechnology and genomics. A passionate and dedicated researcher, he holds numerous patents and awards for his scientific breakthroughs and prides himself on his life-long commitment to making science accessible and understandable to the general public, especially children. One of his foremost goals is bringing hands-on, inquiry-based science to K-12 classrooms.

Dr. Hood earned an M.D. from Johns Hopkins University in 1964 and a Ph.D. in biochemistry from the California Institute of Technology in 1968. Since then, his research has focused on the study of molecular immunology and biotechnology. His interests also include autoimmune diseases, cancer biology and mammalian development. Dr. Hood has published more than 600 peer-reviewed papers and co-authored textbooks in biochemistry, immunology, molecular biology and genetics. He also co-edited “Code of Codes,” a book discussing scientific, social and ethical issues raised by genetic research. Dr. Hood is a member of the National Academy of Sciences, the American Philosophical Society, and the American Association of Arts and Sciences.

His professional career began at Caltech, where he and colleagues pioneered four instruments that constitute the technological foundation for contemporary molecular biology. One of the instruments has revolutionized genomics by allowing the rapid automated sequencing of DNA. Dr. Hood also was one of the first advocates and is a key player in the Human Genome Project — the quest to decipher the sequence of human DNA. He also played a pioneering role in deciphering the secrets of antibody diversity.

In 1992, Dr. Hood moved to the University of Washington to create the cross-disciplinary Department of Molecular Biotechnology, bringing together chemists, engineers, computer scientists, applied physicists and biologists. At the UW, he applied his laboratory’s expertise in DNA mapping to the analysis of human and mouse immune receptors and initiated studies in prostate cancer, autoimmunity, and hematopoietic stem cell development.

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John Hotchkiss
John Hotchkiss is the Chief Technology Officer of AnVil Informatics, a company providing in silico drug discovery services and custom software development. Prior to joining AnVil, Mr. Hotchkiss was CTO at ActiveCyte, Inc., creating Internet-based search and decision-support resources to streamline and optimize the licensing of life science innovations. Prior to ActiveCyte he served as Vice President, Global Engineering at Terra Lycos (previously Lycos, Inc.), the fourth most-visited network of Internet sites in the world. His responsibilities there included product development, quality assurance, international production, and technical infrastructure. Mr. Hotchkiss also served as Director of the Technologies Division and Vice President, Software Tools at Harlequin, Inc. Additionally, Mr. Hotchkiss served five years as contributor and Engineering Manager in the Advanced Technology Group of Apple Computer, Inc. where he managed development efforts on products such as Apple Dylan and the Newton PDA. Mr. Hotchkiss also held software engineer and technical staff positions at Symbolics, Inc., Lisp Machines, Inc., and Itek Optical Systems.

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Michael Hucka, Ph.D.
Dr. Hucka is a researcher and programmer at the California Institute of Technology (Caltech), in the Division of Engineering and Applied Science. He is one of the designers and developers of the ERATO Systems Biology Workbench (SBW), an ongoing project to develop an open-source, integrated software environment for systems biology. Dr. Hucka is also one of the designers and developers of the Systems Biology Markup Language (SBML). SBML is a proposed standard XML-based language for representing biochemical network models in systems biology. It is used as the native format of models communicated between software applications in SBW.

Prior to joining the SBW/SBML development effort, Dr. Hucka was a postdoctoral scholar in the Division of Biology at Caltech. There he worked on GENESIS, a simulation package for neural modeling, and the Modeler's Workspace, a software system for enabling researchers to interact with simulation tools as well as databases of neural models and data.

Dr. Hucka received his Ph.D. in computer science and engineering from the University of Michigan (Ann Arbor, Michigan) in 1998. His Ph.D. research was in the area of computational neuroscience. He received his M.S.E. in computer science and engineering from the University of Michigan in 1991, and Honors B.S. degrees in computer science and in electrical engineering from the University of Utah (Salt Lake City, Utah) in 1986 and 1987, respectively.

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Per Jambeck
Per Jambeck is a Ph.D. student in the Bioengineering department at the University of California, San Diego. He is the coauthor of Developing Bioinformatics Computer Skills (O'Reilly), and he does research on machine learning applications in structural bioinformatics.

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Daniel Joy
Speaker biography coming soon.

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Robert Kehrer
Speaker biography coming soon.

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Craig Kim, Ph.D.
Dr. Craig Kim's primary focus at GeneFormatics is on the development and application of proprietary structure prediction tools for high-throughput sequence analysis. Dr. Kim applies his background in biology and programming towards software design and genome analysis. Prior to joining GeneFormatics, Dr. Kim co-founded Ndex Technologies, a provider of technology consulting and custom software for business-to-business applications. Dr. Kim earned his B.S. from Carnegie-Mellon University and Ph.D. in biochemical engineering from the University of California at Irvine.

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Timothy Kunau
Timothy M. Kunau is on academic staff at the University of Minnesota, where he designs information systems for genomics and computational biology. Tim has worked in high performance computing and research for over fifteen years, holds an MS in Software Engineering, and is now pursuing a Ph.D. Scientific Computation.

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Lorrie LeJeune
Lorrie LeJeune is an editor at O'Reilly and program co-chair of BioCon. She's developing a new series of books in bioinformatics, and at the same time trying to remember everything she's forgotten about biochemistry and molecular biology. In her other, nonbioinformatics life at O'Reilly, she edits books in information architecture, user experience, and web design, and draws many of the animal illustrations featured on O'Reilly books.

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Ann Loraine
Speaker biography coming soon.

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Thomas Madden
Tom Madden leads a team of software engineers at the NCBI that develop and maintain BLAST, a sequence similarity tool. He has been working on BLAST since 1994 at the NCBI. Before coming to the NCBI he performed post-doctoral work in Biophysics.

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David Maddison
David Maddison conceived of the Tree of Life Project, and co-designed and programmed the tools for the original version. He is now coordinator and editor. Along with his brother Wayne, David is an author of MacClade, a software tool for analyzing phylogenetic data, as well as Mesquite, a newer, Java-based, open-source, modular system for phylogenetic analysis. When not staring at a computer screen, David is a biologist who studies the diversity and evolution of beetles, and spends time poking around river shores and looking at beetles under a microscope. He likes implicitly self-referential statements, and is currently tickled by the rebus puzzle "SKIET FLALLME", which does not mean "hard rebus puzzle" in Swedish, although he wishes it did.

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Donna Maglott
Donna Maglott joined NCBI in 1998 to work on databases supporting the RefSeq project and collaborations with the Human Gene Nomenclature Committee (HGNC) and Online Mendelian Inheritance in Man (OMIM), Trained as a molecular biologist, she made the transition to informatics and database management when she assumed responsiblity for several research and support databases at the American Type Culture Collection. At NCBI, she is currently in charge of LocusLink, participates in NCBI's genome annotation pipeline and the development of Map Viewer, and continues to contribute to RefSeq and coordinate interactions among NCBI, HGNC and OMIM.

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Michael J. Martin
Speaker biography coming soon.

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Krista Miller
Krista Miller is the Director of Software Development at INCOGEN, Inc. She has been with the company for three years. She serves as a co-chair of the Technical Architecture working group in the I3C and is also a member of the Technical Operations Committee. Miller graduated from Clemson University in 1999 with a BS in computer engineering and a minor in mathematics.

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Eric Neumann
Eric Neumann is Vice President of Bioinformatics at Beyond Genomics, where he is helping them design and build a multivariate bioinformatics platform, spanning functional genomics, functional proteomics, and metabolic profiling, that is a key component for their Pharmaceutical collaboration projects. He has a proven track record of developing both models and integrative pathway data solutions that are the cornerstone of Beyond Genomics' bioinformatics platform. Dr. Neumann has nearly fifteen years of experience in life science informatics. While at 3rd Millennium, Inc. he was awarded a $2 million ATP-NIST grant for Pathway Informatics. He is co-founder and organizer of the international BioPathways Consortium and is an advisory member of Sun Microsystem's Life Sciences Open-Platform Initiative (I3C), where he is helping them define their Technology Roadmap. He has pioneered the development of new models for use in proteomics, gene profiling and pathway informatics as well ontologies that link major aspects of life sciences together. Along with his team, he is defining new paradigms for bioinformatics where data fusion, advanced data mining, and knowledge assembly are part of a new strategy for Drug Discovery.

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Annalee Newitz
Annalee Newitz (www.techsploitation.com) is a tech writer and activist. By day, she works as the policy analyst at the Electronic Frontier Foundation. During long lunch breaks and late-night coffee jags, she writes the award-winning, syndicated column Techsploitation. She also writes for Wired, Popular Science, Salon, and Security Focus.

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James Ostell, Ph.D.
Dr. James Ostell was first trained in traditional developmental biology and microscopy. He then earned a Ph.D. from Harvard University studying molecular biology. At Harvard he cloned and sequenced at the bench, and also developed software tools for analyzing sequence data. He then developed and supported a commercial package of software for molecular biologists called MacVector, first released in 1982, and still in use today.

In 1988, Dr. Ostell took a position as the Chief of the Information Engineering Branch at the newly formed National Center for Biotechnology Information at the National Institutes of Health. In 1996, he was one of only 12 tenured NIH scientists to be appointed to the Senior Biomedical Research Service.

Under his direction, the NCBI Information Engineering Branch has produced a central computer infrastructure for biomedical information, covering the published literature, DNA and protein sequences, three-dimensional structures of biological molecules, assemblies of complete organism genomes, human genetics and phenotypes, and more.

More that 2 million unique users a month use the NCBI on-line services and the NCBI user community has grown from a base of molecular biology researchers to include physicians, educators, and the general public. Some of the best-known resources provided by NCBI include GenBank, Entrez, PubMed, BLAST, dbEST, UniGene, dbSNP, LocusLink, RefSeq, Human Genome Resources, and many others.

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Glen Otero
Glen Otero received his Ph.D. in Microbiology and Immunology from UCLA in 1995. Otero is the founder and principal at Linux Prophet, a bioinformatics consultancy specializing in the implementation, design, and deployment of Linux Beowulf clusters in the life sciences.

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Dean Pasko
Dean Pasko is a member of the bioinformatics team that has developed the Rat Genome Database. Pasko received his Bachelor degree in genetics from University of Wisconsin-Madison and his Master of Science degree in Management Information Systems from University of Wisconsin-Milwaukee.

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Sandra Porter
Sandra Porter has ten years of experience teaching biotechnology and bioinformatics-related courses and has published an article on using bioinformatics in the classroom. Dr. Porter is currently a senior scientist at Geospiza, Inc. (www.geospiza.com) and develops instructional materials in bioinformatics with funding from the National Science Foundation.

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Yury Rozenman
Yury Rozenman has led a distinguished career in both scientific research and business management on an international scale. He directs the business development effort for the company's dynamic and rapidly evolving life sciences division. Most recently he served as a Sr. Vice President of Supercomputing and Bioinformatics at Juno Online Services. Prior to joining Juno Online Services, he was a Sr. Software Consultant/Strategist at Applied Biosystems Inc. division of Applera Corporation, bringing with him more than 13 years of scientific and bioinformatics experience – predominantly in protein and DNA analysis and its application to understanding biological processes.

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Hannu Saarenmaa
Hannu Saarenmaa is the project manager for information and networking technology at the European Environment Agency in Copenhagen. He manages the European Environment Information and Observation Network that connects environmental agencies and ministries in all European countries into a collaborative and data-sharing network. He is also responsible of the portal of European Community Clearing-House Mechanism under the Convention on Biological Diversity. His development projects include collaborative portal technologies and biodiversity data modeling. Hannu Saarenmaa holds a Ph.D. from the University of Helsinki.

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Dennis Salguero
Dennis Salguero is an independent computer consultant that has presented at computer conferences all around the world and is a frequent contributor to programming books and journals.

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Karla Salguero
Karla Salguero has a Masters degree in Biology and is currently serving a Fellowship at the National Insitute of Health in Washington, DC.

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Peter Schattner, Ph.D.
Peter Schattner was trained as a physicist, but currently works as a computational biologist. He is a member of the computational-biology group at the University of California, Santa Cruz where his principal research interests are in computer-based methods for identifying non-protein-coding-RNA genes. He is also an active developer for the Bioperl project, having designed several of its modules as well as having written the Bioperl tutorial. In his "spare time" he enjoys teaching the use of Perl and Bioperl in bioinformatics.

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Peter St. Onge
Pete St. Onge is a Research Associate in the Emili Lab at the University of Toronto's C.H. Best Institute. Prior to joining the Lab, he developed an environmental information system using open source tools to support his thesis research at McGill University. His primary research interest focuses on the development of explicit methodologies to support scientific research using very large datasets.

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Jason Stajich
Jason Stajich is graduate student in Genetics at Duke University. He is a Core Developer for the BioPerl project and coordinator for the BioCORBA project. Stajich has been a developer with the BioPerl team for 2 years and is author of a number of modules for database and external tool access. He has also co-authored the Ensembl-CORBA implementation to permit non-Perl access to the Ensembl API. His current research interests are in genomics, bioinformatics software development, molecular systematics, and evolution of cis-regulatory sequences.

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Lincoln D. Stein
Lincoln Stein was a hospital pathologist until he saw the light and joined the bioinformatics revolution. He learned the tricks of the trade in Eric Lander's lab at the MIT Genome Center, before striking off on his own at Cold Spring Harbor Laboratory. He is now an associate professor at CSHL and runs a lab, the main interest of which is in integrative databases for biological sciences.

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Jason Stewart
Jason Stewart is the founder of Open Informatics, a bioinformatics software consulting and contracting firm that specializes in Open Source solutions.

Why did Stewart get into bioinformatics? "I was a biologist setting up a high-throughput DNA sequencing facility, and became far more interested in building infrastructure for data communication than actually doing the biology, so I switched fields from Biology to Computer Science."

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Martina Stromvik
Martina Stromvik earned her Ph.D. in Plant Molecular Biology from the University of Illinois at Urbana-Champaign. She is currently a post doctoral researcher at the University of Minnesota's Center for Computational Genomics and Bioinformatics where she explores computational methods of studying plant gene expression. As a natural part of her research, she has acted as an important link between the biologists and the computer scientists developing bioinformatics software.

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Shankar Subramaniam
Shankar Subramaniam is a Professor of Bioengineering and Chemistry and Biochemistry at the University of California at San Diego. He also has a joint appointment at the San Diego Supercomputing Center. Before he moved to UCSD (fall ’99), he was the Director of the computational biology group at the National Center for Supercomputing Applications (NCSA) and a Professor of Biochemistry, Molecular and Integrative Physiology, Chemical Engineering and Electrical & Computer Engineering at the University.

His present research focuses several important aspects of computational biology. These include web-based approaches to bioinformatics, going from protein sequence to structure and function and studying protein recognition and function.

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Christopher Thorpe
Christopher Thorpe is information architect for the Current Science Group, publishers of BioMed Central, Genome Biology and Faculty of 1000. His role encompasses the technical design, architecture, and development of a framework for scholarly publishing which integrates an increasing collection of resources. After a career as a bioinformatician he architected websites for clients such as United International Pictures and Unilever before joining Garland Publishing where he worked on multimedia and electronic delivery of textbooks (Molecular Biology of the Cell). Over two years ago he joined Current Science to architect Genome Biology, a combined web and print journal which includes open-access peer-reviewed research papers and scholarly reviews and then went on to work on BioMed Central. He has a long-standing interest in bioinformatics and in the development of modern forms of publishing in which the research data and methodology, and the peer-reviewed research publication are more tightly integrated and indexed. When not immersed in science publishing he spends his spare time as a volunteer developing the website and e-curation system for a major British sculpture charity.

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Doug Tidwell
Doug Tidwell is a Senior Software Engineer at IBM. He was a speaker at the first XML conference in 1997, and has spoken on technical topics around the world. He works in IBM’s Software Strategy group, evangelizing emerging XML standards such as XForms, SCA and SDO.

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James Tisdall
James Tisdall was Member of Technical Staff at Bell Laboratories in Murray Hill, New Jersey, where he worked in the Information Principles Research Laboratory as a programmer and researcher. He began using Perl in bioinformatics in 1991. In 1992 he released the first version of DNA Workbench, a client/server, multi-platform (PC, Mac, Unix) and parallel processing bioinformatics toolkit written entirely in Perl and served from fifteen Sun servers in the Human Genome Project to hundreds of laboratories worldwide, featuring regular expression search of all of Genbank in 30 seconds. After leaving the Human Genome Project, he led the scientific computing effort at Mercator Genetics; and he led the Bioinformatics Group at Fox Chase Cancer Center. He currently consults for Biocomputing Associates. He is the author of Beginning Perl for Bioinformatics and the upcoming Mastering Perl for Bioinformatics, both from O'Reilly & Associates, as well as several articles and papers in scientific journals. He holds a B.A. in mathematics from City College of New York, an M.S. in computer science from Columbia University, and has held university and dean's fellowships at the University of Pennsylvania and the University of Michigan.

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Bernadette Toner
Speaker biography coming soon.

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Nathan Torkington
Nat Torkington lives and works in New Zealand where he consults on open source and startup strategies, writes for O'Reilly Radar, and co-chairs the Open Source Convention (OSCON).

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Gary Van Domselaar
Gary Van Domselaar is a PhD. Candidate in Dr. David Wishart's research group in the Faculty of Pharmacy and Pharmaceutical Sciences in Edmonton, and a bionformatics Scientist at the Genetics Institute in Cambridge Massachusetts. Gary is a founding member and is currently the Associate Director of Bioinformatics.org.

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William Jay Van Etten III, Ph.D.
Willian Jay Van Etten III is an independent HTC and Informatics Consultant.

Van Etten received his Doctorate of Philosophy in Genetics at Indiana University in Bloomington, Indiana. Following his graduate research, Van Etten was Senior Software Engineer at the MIT/Whitehead Institute Center for Genome Research where he contributed to the genetic mapping of the rat, and was the Head of Informatics for the Mouse Radiation Hybrid Mapping Project as well as Whitehead¹s contribution to the SNP Consortium. Van Etten was involved with the generation of 2 million DNA sequences, and the discovery of 1.4 million Human SNPs; having developed and optimized novel algorithms for SNP discovery.

Van Etten took these high-throughput computing (HTC) research skills to Blackstone Computing as Principal Bioinformaticist where he designed, built and configured HTC environments to support in-silico research for life sciences. Van Etten served as Project Manager for HTC solutions provided to Biogen, Orchid BioSciences, US Genomics, GPC, and the Whitehead Institute, and contributed to HTC solutions provided to Celera Genomics, Astrazeneca, Vertex Pharmaceuticals, Pfizer, Research Genetics, and Partner¹s Health Care.

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Jennifer Weller
Jennifer Weller began her career as a biochemist and molecular geneticist. Frustration with the tools available for handling gene expression data led to a position at the Virginia Bioinformatics Institute where she is leads software development projects focused on EST analysis pipelines, gene expression data storage and analyses, as well as experimental investigations of the genes expressed by plants during root development.

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Travis Wheeler
Travis Wheeler is the lead developer on the project to convert the Tree of Life web site to a dynamically generated, database-driven architecture. When he's not hacking away at the Tree, he's busy with graduate studies in the computer science dept. of the University of Arizona, focusing on computational biology.

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Siamak Zadeh, Ph.D.
Sia Zadeh has held several key positions since joining Sun in April 1994. In 1999, he was named group manager, Life Sciences Group. In this position, Dr. Zadeh's responsibilities include defining the company's strategy and directing its execution of offering for the life science market. Dr. Zadeh was one of the first to identify and exploit the rapid evolution of informatics in the life sciences, and was largely responsible for Sun's early entrance into the life science market. Previously, Dr. Zadeh was a Senior Business Development Manager for Server Product Marketing. In that capacity, he was responsible for Sun's strategic entrance into the high-end technical computing market. Before joining Sun, Dr. Zadeh was a Senior Analyst with Fujitsu America, a computing firm specializing in supercomputers for high-end computing market. Prior to that, he was a Senior Analyst at Atlantic-Richfield Corp. (ARCO) and before that, a Senior Researcher at I.B.M. Dr. Zadeh earned an M.Phil. and a Ph.D. from Columbia University, New York.

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