Bio-IT World and Expo 2009

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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

12:30-4:00pm Pre-Conference Workshop 4*: Recent Advances in Molecular Dynamics: Target Elucidation and Ligand Docking

Ron Dror, Ph.D., Senior Research Scientist, D. E. Shaw Research
Roy Kimura, Ph.D., Senior Scientist, Computer Assisted Drug Design, Bristol-Myers Squibb
Dorothee Kern, Ph.D., Professor of Biochemistry, HHMI Investigator, Brandeis University

*Separate Registration Required


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
Research Computing and Infrastructure Technology

Chris Dagdigian, Founding Partner and Director of Technology, BioTeam, Inc.

 

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
Integrative Genomics

Eric E. Schadt, Ph.D., Executive Scientific Director, Genetics, Rosetta Inpharmatics/Merck Research Labs; Vice President and Chief Scientific Officer, Sage

 

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.
Lutz Weber, Ph.D., CEO,  OntoChem GmbH

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
Howard Feldman, Ph.D., Research Scientist, Research & Development, Chemical Computing Group
PSILO® is a database system that provides an easily accessible, consolidated repository for macromolecular structures, protein-ligand, electron density and related information. It offers research organizations a means to systematically track, register and search both experimental and computational macromolecular structural data. A web-based interface facilitates the searching and accessing of public and private data.  Attendees will learn the benefits of a comprehensive data management solution for structural data, the benefits of mmCIF data representation, how RCSB's ligand dictionary can be used to correct ligand structures, and the importance of version control.



Sponsored by

 

12:30 Luncheon Presentation 
Pantheon: An Open Platform for Cheminformatics and CADD   

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
Personalized Genomics – The Impact of Large-Scale Human Sequencing Projects

Clifford Reid, Ph.D., Chief Executive Officer, Complete Genomics, Inc.

 

8:45 Keynote Panel
The Future of Personal Genomics A special plenary panel discussion featuring:

  • Jorge Conde, Co-Founder & CEO, Knome, Inc.

  • Robert C. Green, M.D., M.P.H. Professor of Neurology, Genetics and Epidemiology, Boston University School of Medicine and Public Health

  • John Halamka, M.D., M.S., CIO, Harvard Medical School

  • Clifford Reid, Ph.D., Chief Executive Officer, Complete Genomics, Inc.

  • Philip Reilly, Third Rock Ventures

  • Dietrich Stephan, Ph.D., Co-founder and Chief Science Officer, Navigenics, Inc.

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 
Learned from Your Peers 
(Joint with Track 3: Predictive and in silico Science)

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. 
2:30 Automated Compound Submission and Active Learning Using HT-ADME in silico Models
Rishi Gupta, Ph.D., Senior Scientist, Computational Sciences Center of Emphasis, Pfizer
We present herein the status of our work towards automated compound submission and active learning. We introduce the concept of “automated submissions”, that is, a mechanism that uses in-silico models and sends only those compounds for screening which it cannot predict with a high level of confidence. This mechanism not only decreases the number of compounds being screened but, also, allows a model to iteratively expand its chemical space where it has limited prediction scope. Co-authors of this work include Stefan J. Steyn of PDM Therapeutic Areas and Eric Gifford of CS CoE. 

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

Video Highlights

White Papers

 

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