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Enabling discovery and improving knowledge management through access to public and commercial science, tools and databases and through the integration of chemical and biological data. Monday, April 27 Ron Dror, Ph.D., Senior Research Scientist, D.
E. Shaw Research 4:00 pm Event Chairperson’s Opening Remarks Cindy Crowninshield, Conference Director, Cambridge Healthtech Institute Keynote Introduction: Microsoft, speaker to be Announced 4:15 Plenary Keynote
5:00 Welcome Reception in the Exhibit Hall Drop off a business card at the CHI Sales Booth for a chance to win 1 of 2 iPods ®!
7:00 Networking Event hosted by BiotechTuesday
Tuesday, April 28
7:30 am Registration and Morning Coffee 8:15 Event Chairperson’s Opening Remarks Phillips Kuhl, Co-founder and President, Cambridge Healthtech Institute Keynote Introduction: caBIG 8:20 Plenary Keynote
9:00 Keynote Presentation & 2009 Benjamin Franklin Award 9:30 Coffee Break, Exhibit and Poster Viewing in the Exhibit Hall
ACCESS: Enabling Discovery through Access to ‘Open Source’ Science, Databases and Software Tools 10:50 Track Chairperson’s Remarks Christopher Southan, Ph.D., EMBL European Bioinformatics Institute (EBI) 11:00 Chemical Biology Databases: Going Beyond Lists of Compounds David DeCaprio, Ph.D., Associate Platform Director for Chemical Biology and Novel Therapeutics, Broad Institute This talk will describe efforts underway at the Broad Institute to improve the consistency, quality, and transparency of stored experimental and other biological data of each compound as well as improved tools to enable more effective access. 11:30 Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry Antony Williams, Ph.D., Founder, ChemZoo, Inc.; Host, ChemSpider This presentation will provide an overview of the issue of quality in many chemistry-related databases, approaches to cleaning up the data, and how a curated platform can become the centralized hub for resourcing information about chemical entities. Sponsored by
 12:00 Tapping Into the Custom Chemistry Space of Chemical Suppliers Attila Bérces, Ph.D., CEO, Omixon Kft.
The custom chemistry space of synthetically feasible compounds of chemical suppliers is orders of magnitudes larger than what they offer off the shelf. OntoChem has developed a database of hundreds of millions of compounds available through two- or three-step synthesis from capable chemical suppliers. Omixon has developed high performance search and library comparison algorithms capable of efficiently handling this amount of data. We present a solution that enables pharmaceutical companies to enrich their compound archive by maximizing its diversity and fill gaps in their chemical space by adding uniquely selected custom synthetic compounds. Why order the same compounds as your competitors? This solution helps companies to enrich their compound archive in a unique way.
Sponsored by
 12:15 PSILO: A Repository for Protein Structural Information 12:30 Luncheon
Presentation
Greg Smith, CTO, Tripos International Pantheon is an affordable, extendable cheminformatics solution that enables discovery scientists to organize, analyze, and visualize chemical and biological data and make better decisions faster. Pantheon addresses many basic cheminformatics workflows and capabilities. It can act as a standalone software application or as a platform for drug discovery workflows, offering easy integration with 3rd party or in-house tools. Attendees will learn about cheminformatics workflows and user scenarios addressed by Pantheon as well as case studies illustrating Pantheon as a platform for drug discovery. Co-authors of this work include Greg Smith and Stephan Nagy of Tripos International.
SCREEN: Screening and Modelling: Success Stories and the Challenges that Remain 1:40 Chairperson’s Remarks Andreas Bender, Ph.D., Assistant Professor, Medicinal Chemistry Division, Leiden / Amsterdam Center for Drug Research 1:45 Proteochemometrics Modeling: A Technique to Predict Activities Simultaneously Against Multiple Receptors / Mutants and Applications to Non-Nucleoside Reverse Transcriptase Inhibitors Andreas Bender, Ph.D., Assistant Professor, Medicinal Chemistry Division, Leiden / Amsterdam Center for Drug Research Proteochemometrics Modeling involves ligand- as well as target-features for generating activity models. This talk will provide insight into a novel modeling method which can be applied also to in-house datasets. 2:15 Virtual Screening at the Fragment Level Zenon Konteatis, Ph.D., Senior Scientist, Computational Chemistry, Locus Pharmaceuticals, Inc. Virtual screening at the fragment level instead of the molecule level has the same advantages as its experimental counterpart. This talk will present a computational method that addresses each of these key elements and show case studies that demonstrate their overall efficacy in virtual fragment screening and the subsequent de novo design of molecules from the screening results. 2:45 Findings and Discussion of the Challenge to Predict Aqueous Solubility Held by the Journal of Chemical Information and Modeling Anton Hopfinger, Ph.D., Professor, University of New Mexico, Editor, Journal of Chemical Information and Modeling Recently the Journal of Chemical Information and Modeling (JCIM), held a Challenge to predict the aqueous solubility of 32 structurally diverse compounds based upon a training set of 100 compounds and any additional information contestants wished to employ. The entries have been scored and the findings are posted on the JCIM website. This presentation will further report findings from the Challenge, comments regarding the findings from contestants and preliminary thoughts of Journal editors regarding the Challenge and possible future prediction challenges. 3:15 Refreshment Break, Exhibits and Poster Viewing in the Exhibit Hall
MANAGE: Coping with the Volume of Data and Transforming it into Knowledge 3:45 Gaining Efficiencies through Open Innovation Susie Stephens, Ph.D., Principal Research Scientist, Eli Lilly & Co. This talk will examine how the industry can benefit from enabled decision making through open innovation, as well benefiting from data explosion, mining and linking knowledge, increasing uptake of new ideas, and easing barriers to collaboration. 4:15 Implementation and Uses of a Next Generation Discovery Informatics System David Nunn, Ph.D., Principal Research Scientist, ChemInformatics, Wyeth Research The NextGen project at Wyeth has been a large scale reinventing of our Discovery informatics data access and analytics capabilities. This presentation discusses how Wyeth scientists have worked closely with IS staff and external partners Tripos and Accenture to achieve these goals. 4:45 Leveraging Data Pipelining for On-the-Fly Data Integration of Multiple Experiments Jeremy L. Jenkins, Ph.D., Research Investigator, Lead Discovery Informatics, Novartis Institutes for BioMedical Research Data generated by project teams in the pharmaceutical industry is often held in data silos with the single-minded purpose of supporting one project. However, with even basic semantic standardizations in place, prospective lead finding may be driven by integrating historical data collected across multiple experiments as well as combining internal and external data sources to train probabilistic models and make new predictions. 5:15 2009 Best of Show Awards in Exhibit Hall 6:15 Exhibit Hall Closes 6:30 2009 Bio-IT World’s Best Practices Awards/Dinner
Wednesday, April 29
7:30 am Registration and Morning Coffee 8:00 Event Chairperson’s Opening Remarks Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World 8:05 Plenary
Keynote
8:45 Keynote Panel
9:45 Coffee Break, Exhibit Viewing, Vendor Theater Presentations, and Poster Competition in the Exhibit Hall
INTEGRATE: Integrative Approaches for Chemical and Biological Data and Knowledge Management 10:45 Chairperson’s Remarks Richard Cramer, Ph.D., Senior Vice President, Science & Chief Scientific Officer, Tripos 11:00 Comparing Public and Commercial Databases of Bioactive Chemicals by Content and Compound-to-Protein Mappings Christopher Southan, Ph.D., EMBL European Bioinformatics Institute (EBI) This talk compares content from selected public and commercial databases and reviews the different strategies used for extracting unstructured data from documents describing bioactive compounds and transferring them to structured relational databases for high value data mining. 11:30 Open Semantic Data in Science Peter Murray-Rust, Ph.D., Professor, Chemistry and Molecular Informatics, University of Cambridge, Senior Research Fellow, Churchill College Science is increasingly dependent on data and Bioscience has led the world in exposing its data in Open Semantic form (genomes, sequences, proteins, etc.). This allows the power of the Semantic Web (Berners-Lee 2001) to use ontologies and inference to support scientific discovery and reasoning. In contrast much chemistry is hidden behind commercial firewalls or proprietary formats which prohibit their integration into the Semantic Web. I shall show what needs to be done to make chemical data (structures, reactions) fully available to bioscience; when this is done we can expect a major increase in our understanding of biology at the molecular level. 12:00 pm Open Source Cheminformatics: Tools and Data Rajarshi Guha, Ph.D., Visiting Assistant Professor, Informatics, Indiana University This talk highlights the current options for open source cheminformatics software, focusing more on toolkits (CDK and OpenBabel) and platforms (such as Bioclipse and R). Issues to be addressed include what they provide, problems with their usage, and support infrastructure. 12:30 Luncheon in the Exhibit Hall 2:00 Exhibit Hall Closes
EXECUTE: Case Studies and Lessons 1:55 Chairperson’s Remarks Jeremy L. Jenkins, Ph.D., Research Investigator, Lead Discovery Informatics, Novartis Institutes for BioMedical Research 2:00 Power to the People: Integrating Data and Analysis in One Easy Application Derek Debe, Ph.D., Senior Group Leader, Scientific Informatics and Automation, Abbott Laboratories This talk discusses the
successful development and deployment of a Drug Discovery data integration
and analysis platform at Abbott Laboratories. Specific use case examples
will be presented, including functionality useful for Hit-to-Lead analysis
and Lead Optimization efforts. 3:00 Predictive In-Silico Science: Shifting the Discovery Paradigm Yossi Cohen, M.D., VP R&D, Compugen We share insights into how new in silico predictive approaches differ from the traditional discovery approaches, and why it has the potential to predict high-quality candidates in a much more efficient and cost-effective manner. Through examples of some of Compugen's successes in drug candidate discoveries, this talk will demonstrate how the predictive in silico approach is steadily revolutionizing the R&D paradigm of the industry. We will highlight the potential of in silico science to increase success rates in the preclinical stages of drug development and how collaborative efforts can help stem clinical stage attrition. 3:30 "Virtual Fragment Linking": An Approach to Identify Potent Binders from Low Affinity Fragment Hits Meir Glick, Ph.D., Research Investigator II, Lead Discovery Informatics, Novartis Institutes for BioMedical Research We explore the possibilities of using fragment-based screening data to prioritize compounds from a full HTS library, a method we call virtual fragment linking (VFL). The ability of VFL to identify compounds of nanomolar potency based on micromolar fragment binding data was tested on 75 target classes from the WOMBAT database and succeeded in 57 cases. Further, the method was demonstrated for seven drug targets from in-house screening programs that performed both FBS of 8800 fragments and screens ofthe full library. VFL captured between 28% and 67% of the hits (IC50 < 10?M) in the top 5% of the ranked library for four of the targets (enrichment between 5-fold and 13-fold). 4:00 Conference Adjourns |
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Chris Dagdigian, Founding Partner and Director of Technology,
BioTeam, Inc.
Eric E. Schadt, Ph.D., Executive Scientific Director, Genetics, Rosetta Inpharmatics/Merck Research Labs; Vice President and Chief Scientific Officer, Sage
Clifford Reid, Ph.D., Chief Executive Officer, Complete Genomics,
Inc.
