4:00 pm Event Chairperson’s Opening Remarks
Cindy Crowninshield, Conference Director, Cambridge Healthtech Institute

4:15 Informatics: Integration & Convergence
John Reynders, Ph.D.,Vice President & Chief Information Officer, Johnson & Johnson, Pharma R&D

5:00 Welcome Reception in the Exhibit Hall
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7:30 am Registration and Morning Coffee

8:15 Event Chairperson’s Opening Remarks
Phillips Kuhl, Co-founder and President, Cambridge Healthtech Institute 

8:20 Drug Development: Evolving Challenges and Opportunities
Joshua Boger, Ph.D., President & Chief Executive Officer, Vertex Pharmaceuticals, Inc.

9:00 Keynote Presentation & 2008 Benjamin Franklin Award 
Robert Gentleman, Ph.D., Head of Program in Computational Biology, Fred Hutchinson Cancer Research Center

9:30 Coffee Break, Exhibit and Poster Viewing in the Exhibit Hall

10:50 Track Chairperson’s Remarks
Kathryn Loving, Ph.D., Applications Scientist, Shrödinger, Inc.

11:00 Merging High-Content Screening and in silico Approaches for Compound Profiling and Mode-of-Action Analysis
High-content screening observes the reaction of a cell to an administered compound by multidimensional micros-copy and it provides a potentially more information-rich complement to single-readout conventional assays. On the other hand, microscopy-based screening can also be more ‘opaque’ in the way that no mechanistic explana-tion for the observed effect is provided per se. By merging high-content screening with in silico target prediction, we present a method to merge the best of both worlds: by high-content screening we are able to observe the systems response, while at the same time providing hypotheses for the observed effects via the predicted targets of compounds. We screened more than 6k compounds in high-content screenings and discuss cases where the phenotypic response and the predicted targets agree with each other, but also the even more interesting ‘atypi-cal’ cases where similar phenotypes are observed by very different predicted targets (which might for example be located in the same pathway).
Andreas Bender, Assistant Professor for Cheminformatics, Leiden/Amsterdam Center for Drug Research and No-vartis Institutes for BioMedical Research, Inc.

11:30 Elucidating Activity in Primary Screens Using Diversity-Oriented Chemical Libraries 
This talk will explore how the Broad Institute Chemical Biology and Novel Therapeutics platforms are creating chemical libraries using diversity-oriented synthesis and are performing high throughput screening on those li-braries using phenotypic, cell-based screens to look for potential leads and probe compounds. This approach al-lows projects to begin with a much richer data set and enables more intelligent design of follow-up studies. Data generated within the platform are made publicly available through our website, Chembank, which also provides rich tools for cross-sectional analysis of screening data. 
David DeCaprio, Director of Informatics, Chemical Biology and Novel Therapeutics, Broad Institute/MIT

12:00 Large-Scale Annotation of Small-Molecule Libraries Using Public Databases
The recent rapid expansion of the NIH PubChem database provides an opportunity to link existing biological data-bases with compound catalogs and provides relevant information that potentially could improve the information garnered from large-scale screening efforts. We will demonstrate an annotation pipeline based on integrating multiple databases. We will also discuss how annotations can be applied to in-house HTS databases in identifying signature biological inhibition profiles of interest and expediting the assay validation process. The automated an-notation of thousands of screening hits in batch is becoming feasible and has the potential to play an essential role in the hit-to-lead decision making process.
Yingyao Zhou, Ph.D., Director of Informatics, Genomics Institute of the Novartis Research Foundation

12:30 Luncheon Workshop (Sponsorship Available) or Lunch on Your Own

1:45 Structure-Based Drug Discovery of CDK2 Inhibitors
A series of pyrazolopyrimidines- and imidazopyrazines-containing inhibitors of CDK2 was discovered through high-throughput screening. The crystal structures of these inhibitors and two more related bicyclic cores show that there are is a dominant binding mode featuring hydrogen bonds to the backbone of the kinase hinge region. Even though ab initio computations indicated that the imidazopyrazine core would bind more tightly to the hinge, pyrazolopyrimidines gain an advantage in potency through an H-bond network involving two catalytic residues and bridging water molecules. Further insight into inhibitor/CDK2 interactions was gained from analysis of addi-tional crystal structures and significant improvements in potency were realized by optimization of hydrophobic substituents into the gatekeeper region of the ATP binding site. Good selectivity was achieved by the most potent inhibitors.
José S Duca, Ph.D., Principal Scientist, Schering-Plough Research Institute

2:15 Protein-Protein Interactions Involving Macrocycle Compounds
Ensemble Discovery uses DNA programmed chemistry to generate large numbers of macrocycle compounds. This technique creates molecules with attached instructions, encoded in a piece of DNA, of how that molecule was built. This DNA is used as both a barcode to quantitatively identify the amount of each molecule during a biochemical screening process and to identify the most active molecule structures. This data allows SAR analysis and the development of additional compounds, to further improve binding and specificity. We have focused on macrocycles because they present a larger surface area than traditional small ‘rule of 5’ compliant molecules, and can bind shallow clefts on protein surfaces involved in protein-protein interactions that are traditionally only addressed by large biologics.
Nathan Walsh, Ph.D., Principal Informatics Scientist, Ensemble Discovery Corporation

2:45 Computational Development of Allosteric Small Molecule Antagonists of RecA Fibril Formation
Frank Guarnieri, Ph.D., Chief Scientific Officer, Solmap Pharmaceuticals
In response to bacterial DNA damage from UV or antibiotics, dozens of RecA subunits homo-oligerimize seeding onto single-stranded DNA and effect an ATP driven repair. Computational solvent mapping identified a class of small molecules (200 MW) predicted to have high affinity for the allosteric site. Two molecules were purchased from Sigma, one predicted to have high affinity for the site and the other, a closely related analog, predicted to have no affinity for the site. Bacterial growth assays confirm the computational predictions, but direct binding assays give hard to interpret results. The importance, complexity and potential for targeting RecA as a means of dealing with the growing problem of resistance will be discussed.

3:15 Refreshment Break, Exhibit and Dedicated Poster Viewing

3:45 CONTOUR: Drug Discovery Platform 
CONTOUR was developed with the concept of creating a new generation of structure-based design technology tightly integrated with medicinal chemistry. It allows us to generate thousands of possible novel designs and visualize most relevant ones with chemists. The goals of the design are to generate novel ideas, explore wide range of chemistries, assess synthetic feasibility, increase potency and selectivity, minimize off-target activity, and design against metabolic activation and toxic liabilities. We will discuss our technology platform, and its ap-plication to the therapeutic programs.
Suresh Singh, Director, Computational Drug Design, Vitae Pharmaceuticals

4:15 Introducing Canvas, Schrödinger’s New Cheminformatics Platform
The successful application of cheminformatics tools in drug discovery requires not only the right science but also the right integration. Schrödinger has developed a new cheminformatics platform, Canvas, which has a wealth of modular cheminformatics tools with an open API so they can be easily integrated with existing interfaces, such as the open source workflow tool KNIME, or used through the Canvas interface.
B. Woody Sherman, Ph.D., Director of Applications Science, Schrödinger, Inc.

4:45 Side Effect Profile Prediction - How to Deal With Drug Safety Issues Early On
This talk will describe a novel method to predict adverse side effects from the chemical structure only. By em-ploying clinical databases along with chemical information, the chemical features can be identified that are most likely the reason for a certain side effect. This information can then be employed in early drug discovery.
Josef Scheiber, Ph.D., Postdoctoral Fellow, Lead Discovery Informatics/Safety Profiling, Novartis Institutes for Biomedical Research Center & Research Institute

5:15-6:15 2008 Best of Show Awards/Reception in the Exhibit Hall 

6:15 Exhibit Hall Closes 

7:00 2008 Bio-IT World’s Best Practices Awards/ Dinner 

7:30 am Registration and Morning Coffee

8:00 Event Chairperson’s Opening Remarks
Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World 

Keynote Introduction: 
Ron Ranauro, President and CEO, GenomeQuest, Inc. 

8:05 Personalized Genetics: Advancements & Driving Change
Linda Avey, co-Founder, 23andMe, Inc..

8:45 The Future of Personal Genomics George Church, Ph.D., Professor of Genetics and Director of the Center for Computational Genetics, Harvard Medical School Dietrich Stephan, Ph.D., Co-founder and Chief Science Officer, Navigenics, Inc. Jeffrey M. Drazen, M.D., Editor-in-Chief, New England Journal of Medicine; Distinguished Parker B. Francis Professor of Medicine, Harvard Medical School Fred D. Ledley, MD, Professor and Chair, Bentley College; Founder and Chairman, My Genome John Halamka, MD, MS, CIO, Harvard MedicalSchool Linda Avey, co-Founder, 23andMe, Inc.

9:45 Coffee Break, Exhibit Viewing, Vendor Theater Presentations, and Poster Competition in the Exhibit Hall
QSAR & Lead-Hopping

10:45 Track Chairperson’s Remarks
Matthew Stahl, Ph.D., Senior Vice President, Head of Strategic Development, OpenEye Scientific Software

11:00 Technology Highlights

11:30 Lead-Hopping and Beyond
When “lead-hopping”, to identify for example a backup series, recent head-to-head comparisons indicate that li-gand shape similarity searching is significantly more effective than docking or Tanimoto 2D fingerprints. 
This finding is one of several enhanced drug discovery capabilities that the topomer technologies are enabling: exhaustive searching of 10^20 synthetically more accessible structures, in hours; robust and automatable 3D-QSAR based optimization of biological profiles; computationally addressing synthetic cost as well as biological benefit; and, improved forecasting of off-target biological responses. This talk will explore newly available cheminformatics approaches that offer a wide range of relatively well validated benefits to the different stages of a drug discovery project.
Richard Cramer, Ph.D., Chief Scientific Officer, Tripos

12:00 pm Technology Highlights (Sponsorship Available) 
Better appreciate the interplay of the research and technology drivers impacting pharmaceutical and biotechnol-ogy companies, and learn to apply them productively within your own organizations. Find out more about these products and services to help you tackle your daily challenges. For sponsorship information, contact Katelin Fitz-gerald at kfitzgerald@healthtech.com. 

12:30 Luncheon in the Exhibit Hall

2:00 Exhibit Hall Closes

2:10 Chairperson’s Remarks
Kevin Davies, Ph.D., Editor-In-Chief, Bio-IT World

2:20 How the Three Pillars of Agility in Research Informatics Support R&D Productivity
Juergen Hammer, Ph.D., MBA, Global Research Informatics Director, Global Head, In Silico Sciences, Nutley Head, Group Research Information (GRI), GRI Liaison to Pharma Research, F. Hoffmann-La Roche Inc.
Does the relatively high investment that increase the efficiency of drug discovery reflect the true informatics needs of drug discovery organizations today? For example, our process biology concept contributed to increased efficiency via request handling, routine analysis flows and results databases, and the possibility to integrate and share results company-wide via gene and target-centric portals. However, significant value-add observed over several years resulted mostly from research informaticians who rapidly customized analysis flows – often manually and with some trial and error - according to scientific problems and disease context. The results were scientific discoveries (reagents, targets, biomarkers, compounds) as compared to more traditional laboratory efficiency increases. Despite a higher value proposition, these complex scientific computations were mostly “one-offs” lacking scalability. In an effort to better balance our informatics efforts towards these value-adding activities, we introduced an operational model that combines scientific excellence with flexible operations and the use of informatics agility platforms. We will discuss the benefits and challenges of this model

2:50 Dynamic Delivery of Services Through Just in Time Application
Chris Waller, Ph.D., Senior Director, Chemical Sciences Platforms, Research and Development Informatics, Pfizer Global Research and Development
The last few years has seen a focus on the greater adoption of a service oriented architecture philosophy within the software development community of practice. The migration from legacy two-tier systems to n-tier systems with distinct middle tier services has necessitated an era of application deconstruction. Service oriented architecture (SOA) is all about “verbs” from my group’s perspective (e.g., register, query, display, etc.), and we have filled our mid-tier with these valuable reusable encapsulated services. As a technology manager, this work is appealing from an application development and support perspective. However, as a solution provider, whose value to the organization is tied very tightly to the business value delivered by my services, this work has had limited impact. This last statement has both positive and negative interpretations in that off-loading services from thick clients into the mid-tier should have no beneficial or detrimental impact on the end-user experience if the work is done properly. Having laid the foundation in the middle tier, we are now refocusing our attention back on the client. This presentation will review my vision to create business process focused applications that deliver services to the end-users in a flexible and dynamic manner.

3:10 Growing ABCD in the Research & Early Development World
Edward P. Jaeger, Ph.D., Director, Research & Early Development Information Technology, Johnson & Johnson Pharmaceutical Research
This talk will highlight recent developments in ABCD, an integrated drug discovery informatics platform developed at Johnson & Johnson Pharmaceutical Research & Development, L.L.C. ABCD is an attempt to bridge multiple continents, data systems and cultures using modern information technology, and provide scientists with tools that allow them to make informed, data-driven decisions. The first phase of ABCD focused on decision support (data warehousing, retrieval, analysis and visualization) and met with great success, becoming an indispensable tool for more than 1,200 users across all J&JPRD research sites. The system consists of two major components: a data warehouse, which combines data from multiple chemical and pharmacological transactional databases, designed for supreme query performance and a state-of-the-art application suite, which facilitates data upload, retrieval, mining, and reporting. Chemical intelligence, performance, and analytical sophistication lie at the heart of the new system, which was developed entirely in-house. ABCD has delivered on its promise of simplifying data assembly, delivery, comparison and decision-making. It has also driven business process change to create more consistent and better-documented data for discovery analysis. We have now embarked on the development of a new global transactional system that will replace the legacy operational data stores. This presents us with several compelling advantages: an ability to create a common ontology used across the transactional and decision support layers, a simpler, more streamlined and more robust ETL, and a radically different end-user experience through the use of a single, unified application front-end. Indeed, ABCD utilizes a common framework for the entire research data life cycle, including processing, upload, mining, analysis, visualization and reporting.

3:40  Refreshment Break in the Exhibit Hall

4:00 Management of Non-Clinical Study Data
David M. Sedlock, Ph.D., Director Research Systems, Millennium Pharmaceuticals Inc.
The generation of pre-clinical data presents a unique problem for researchers related to data creation, storage, access, and reporting. These data are generally part of a development portfolio consisting of both GLP and non-GLP studies with different data handling requirements generally in place for each study type. This presents a conundrum when looking at overall data management needs due to differing requirements for system validation, archiving strategies, etc. The presentation will look at this issue in some detail to examine ways to address the problems encountered when attempting to integrate these disparate data types.

4:30 Building Bridges Across the Divide
Ingrid Akerblom, Ph.D., Executive Director, Merck Research Labs IT, Clinical Development
To achieve the promise of Biomarkers to transform discovery research and increase our ability to provide patients value through targeted medicines, there must be a focus on building integrated knowledge across the entire drug development cycle. In addition, there is increased recognition that much of this knowledge exists outside the walls of the pharmaceutical industry. We are piloting integration solutions involving both internal and external partners across several domains such as Clinical Development and Discovery Research to determine how to derive the most value from information connectivity. The successes and the challenges will be discussed.

5:00 Panel Discussion: INDUSTRY OVERVIEW

INTEGRATION OF INFORMATICS IN SUPPORT OF DISCOVERY, DEVELOPMENT & PRODUCTION - WHAT DOES THE FUTURE HOLD?

Panel Moderator: Joe Cerro, President & Founder at The Schooner Group, LLC
Panelists: All of the above speakers