Launching A Bioinformatics Program At Roosevelt University V2

Launching a Bioinformatics Program at Roosevelt University Ogan Gurel, MD MPhil Adjunct Professor 13 January 2005

Outline • Setting the stage • Mission • Strategy • Resources • Plan

What is bioinformatics? • What is Bioinformatics? - Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. • What is Computational Biology? - The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.

Information Flows in Biology • The Central Dogma – – – –

Genomics Proteomics Structural Bioinformatics Cellular, organism, population and ecosystem information flows

• The Scientific Method – – – –

Create hypotheses Design experiments Evaluate data and Extend/modify hypotheses

Major U.S. Bioinformatics programs California New Jersey • Stanford University Biomedical Informatics • Graduate Program Studies in Computational • • •

UCSD Bioinformatics and Computational Biology, Department of Bioengi New York Keck Graduate Institute, Professional Masters in Applied Biosciences • Columbia University Department of UC-Berkeley Program in Genomics and Computational Biology

Connecticut •

Bioinformatics at Yale

Illinois •

University of Illinois at Urbana-Champaign – Center for Biophysics and Computational Biology – W.M. Keck Center for Bioinformatics

Massachusetts •

MIT Whitehead Center for Genome Research

Pennsylvania • •

Keck Center for Advanced Training in Computational Biology Penn State University Center for Computational Biology

Texas •

W.M. Keck Center for Computational Biology at Rice University

Tennessee • Biomedical Informatics at Vanderbil

Bioinformatics programs in Illinois

• Bioinformatics at University of Illinois at C • University of Illinois at UrbanaChampaign

– Center for Biophysics and Computational Bio – W.M. Keck Center for Bioinformatics

• University of Chicago • Northern Illinois University

Why Roosevelt? • Existing industry-oriented successful Biotechnology program • Many of the core courses are already offered • Relatively little capital required to establish a research program • Relatively strong industrial base – Abbott pharmaceuticals, biotech, hospital industry • The university has flexibility to accommodate this intrinsically

The Mission for Bioinformatics at Roosevelt • Strong core program of bioinformatics • Training students for professional careers in industry • Establishing a practically-oriented research program

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A possible model: The Northeastern Bioinformatics Master’s program http://www.bioinformatics.neu.edu/ About the Program We are experiencing an unparalleled boom in the already significant biotechnology and pharmaceutical industries, particularly in the Boston area. A January 1999 study by the accounting firm Ernst & Young shows that New England area has surpassed San Francisco, in the formation of firms searching for gene-based drugs. It is estimated that the Massachusetts biotechnology industry now employs triple the number of employees that it did in 1991 (25,000 currently and increasing). Our practice-oriented, professional M.S. Program in Bioinformatics therefore has a strong foundation in our geographical region. The explosion in genomic information and in the elucidation of metabolic and signaling pathways of various cell types has created an unprecedented, but largely unmet, need for professionals with a working knowledge of the biological sciences and computational methods. The shortage, which is especially severe in the biotechnology and pharmaceutical industries, has been discussed in the press and at workshops. We can expect a comparable demand in hospital and other clinical settings as the impact of new technologies diffuses into clinical research and medical practice. The change has been so rapid that universities have been caught unprepared: few offer suitable courses, and virtually none offer a well integrated curriculum that meets the needs that are sure to grow and evolve as life sciences become increasingly conceptual and quantitative. This Northeastern University M.S. Program in Bioinformatics is designed to address these needs through interdisciplinary training that bridges departments, colleges, and universities, includes industrial internships, and educates professionals who are prepared for immediate productivity in industrial or clinical settings.

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Curriculum Our curriculum has four parts (Fundamental Courses, Core Courses, Internship, Electives) with a total of 32 points. All courses are available in the late afternoon or evening to accommodate student who are employed during the day.

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Fundamental Courses BIOG300 Graduate Biochemistry (4) BIOG301 Molecular Cell Biology (4) MTHG340 Statistics for Bioinformatics (4) CSG100 Data Structures (4)

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All of these courses are required but students with strong backgrounds in either the biological sciences or the computer/information sciences will be exempted from these courses as appropriate.

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Core Courses BIOG381 Ethics in Biological Research (2) CSG102 Database Management (4) BIOG302 Bioinformatics Methods and Algorithms (5) SCG100 Concepts in Pharmaceutical Science (2) BIOG506 Bioinformatics Internship Tutorial (1) BIOG385 Bioinformatics Seminar (this course taken twice) (2)

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Electives At least one four point elective. More electives will be available to students who have been exempted from more than two fundamental courses. A wide range of electives is available including advanced work in computer science, mathematics and biology.

Strategy • Phase Ia Offer bioinformatics as a concentration option with the existing biotechnology program – –

Easy to accomplish Further differentiates for and builds competitive advantage with the existing biotechnology program

• Phase Ib Offer bioinformatics as a certificate program • Phase Ic In parallel, establish one or two research programs – – –

Relatively easy to accomplish Builds competitive advantage Attracts faculty

• Phase II Offer full professional master’s program in bioinformatics • Phase III Offer a medical informatics program – – –

Meets longer-term anticipated demand in this field Coordinate with a hospital/medical school More readily tied into biomedical research funding including bioterrorism

Resources: Present faculty • Sathees Chandra (Biology) • Ogan Gurel (Biology & Mathematics) • James Kenevan (Computer Science) • Robert Seiser (Biology) • Yao Wang (Mathematics) • Cornelius Watson (Biology) • Ray Wright (Computer Science)

Resources: Potential Advisors • Phil Bourne, UCSD (structural bioinformatics) – has agreed to be an advisor • Ted Shortliffe, Columbia (medical informatics) – has expressed interested in being an advisor • Wayne Hendrickson (structural biology), Columbia • Ilhan Dilber (computational fluid dynamics), Fluent USA • Leon Glass (mathematical modelling), McGill

Resources: Funding I • Private – National • Keck Foundation • Burroughs-Welcome Foundation

– Local • Industry (e.g. Abbott) • Illinois Biotechnology Industry Organiation (IBIO) • Local foundations (McCormick – Tribune, Pritzker, etc.)

Resources: Funding II • Government – Federal • NIH Protein Structure Initiative • NSF Information Technology Research program • NIH Biomedical Information Science and Technology Initiative (BISTI) http://www.bisti.nih.gov/

– State • Department of Labor (BiTmap) • Other state initiatives

Epilogue