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Chemical Informatics and Bioinformatics Programs at Indiana University

Chemical Informatics and Bioinformatics Programs at Indiana University. Gary Wiggins School of Informatics Indiana University ACS, Philadelphia, 23 August 2004. Overview. Comments on Chemical Informatics as a Discipline Other Programs and Courses Indiana University Programs Problems

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Chemical Informatics and Bioinformatics Programs at Indiana University

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  1. Chemical Informatics and Bioinformatics Programs at Indiana University Gary Wiggins School of Informatics Indiana University ACS, Philadelphia, 23 August 2004

  2. Overview • Comments on Chemical Informatics as a Discipline • Other Programs and Courses • Indiana University Programs • Problems • Bioinformatics Programs • Future

  3. Comments on Chemical Informatics as a Discipline

  4. Jürgen Bajorath on Chemoinformatics, etc. • Chem-, chemi-, or chemo-informatics • Focus on the information resources needed to optimize the properties of a ligand to become a drug (Frank Brown, 1998) • Decision support by computational means • Drug discovery • Chemical Informatics: the application of information technology to chemistry (not with a specific focus on drug discovery)

  5. Related Terms per Bajorath • Chemometrics • Application of statistical methods to chemical data and the derivation of relevant statistical models and descriptors • Increasingly difficult to distinguish between chemometrics and chemoinformatics • Discovery informatics—acknowledges that gaining knowledge from chemical data alone is insufficient for success in drug discovery

  6. Bajorath’s Conclusions • Boundaries between bioinformatics and chemoinformatics are fluid • Both should be closely combined or merged to significantly impact biotechnology or pharmaceutical research Bajorath, Jürgen, Ed. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery. (Methods in Molecular Biology; 275) Humana Press: Totawa, NJ, 2004.

  7. Other Programs and Courses

  8. Another Program in the US • University of Massachusetts, Lowell • MS in Computer Science with an option in Bio/Cheminformatics • Prescribed courses for 30 hours (assuming all prerequisites met) • Thesis may count for 6 of the hours • Repesentative course: Selected topics in Chemistry: Protein and Chemical Informatics • Also offer a Doctor of Science degree • http://genome.uml.edu/programs_grad.htm

  9. Selected Courses in Cheminformatics • Introduction to Chemoinformatics Course at the University of Michigan • Offered through the interdisciplinary program in Pharmaceutical Engineering • Taught by David Wild • http://www-personal.engin.umich.edu/~wildd/chemoinf/index.html • Chemoinformatics Course at The Danish University of Pharmaceutical Sciences http://www.dfh.dk/phd/courses/descriptions/courses20042005/chemoinformatics.htm • Analytical Informatics at Purdue (Randy Julian) http://miner.chem.purdue.edu/

  10. Bogus Programs??? • Institute of Cheminformatics Studies http://www.cheminformaticscentre.org/chem/ • NC State University Certified Bioinformatics Specialist: Cheminformatics http://www.ncsu.edu/ctu/documents/pdfdocs/marketingpackets/biochembrochure.pdf • Chemoinformatics National BioInformatics Institute http://www.bioinfoinstitute.com/chemoinfo.htm

  11. Indiana University Programs in Chemical Informatics

  12. Specialized Chemistry Degree Options at Indiana University • BS in Informatics with a chemistry or biology cognate (essentially a minor) • MS in Chemical Informatics • MS in Bioinformatics • PhD in Science Informatics (expected Fall 2005) http://www.informatics.indiana.edu • MLS or MIS with a specialization in chemical information http://www.slis.indiana.edu

  13. IU’s MS in Chemical Informatics • Developed jointly by the School of Informatics and chemistry departments at IUB and IUPUI • First students admitted at IUPUI in fall 2001 and at IUB in fall 2002 • Graduates: 4 • Currently enrolled: 11

  14. Unique Program at IUPUI • Laboratory Informatics track at IUPUI • Instrumentation and data interfacing • Laboratory notebooks • Laboratory Information Management Systems (LIMS)

  15. Why IU for Chemical Informatics? • Outstanding Faculty • Excellent computer facilities and infrastructure • Close proximity to major pharmaceutical companies (Lilly, Abbott, Pfizer) and to chemical informatics companies (Tripos, LeadScope, Chemical Abstracts Service) • History of innovative, IT-based chemical information services (QCPE, MSC) • Well-established programs in IU’s SLIS

  16. Core and Affilated Faculty at IUB • MU-HYUN (MOOKIE) BAIK • SANTIAGO SCHNELL • DAVID WILD (visiting) • DIMITRIS AGRAFIOTIS (adjunct) • JOHN BARNARD (adjunct) • JOHN C. HUFFMAN (adjunct) • GEORGE W. A. MILNE (adjunct) • PETER ORTOLEVA (adjunct) • GARY WIGGINS (adjunct) • KEVIN GILBERT (affiliated) • CHARLES H. DAVIS (affiliated)

  17. Core and Affilated Faculty at IUPUI • SAM A.F. MILOSEVICH • MAHESH MERCHANT • JOHN MCKELVEY (adjunct) • DON BOYD (affiliated) • KELSEY FORSYTHE (affiliated)

  18. Outreach Activities • Research relationships with • IU School of Medicine • IUB/IUPUI bioinformatics and proteomics research programs • Commercial firms through internships (LeadScope, Rosetta Inpharmatics, Lilly)

  19. IU Undergraduate Courses • Four one-credit undergrad courses • C371 Chemical Informatics I • C372 Chemical Informatics II: Molecular Modeling • C471 Chemical Information Sources and Services • C472 Computer Sources for Chemical Information

  20. IU Graduate Courses • Two three-credit graduate courses • C571 Chemical Information Technology • C572 Molecular Modeling & Computational Chemistry • New courses under development • Programming for Chemical Informatics • Information Retrieval from Chemistry and Life Sciences Databases

  21. Tools Used or Planned for Use • Spotfire • ChemTK Lite • Chemaxon’s Marvin • Chemical Computing Group’s MOE • Daylight Toolkit • OpenEye (all modules) • BCI software • WaveFunction’s Spartan • Serena Software’s PCModel • [MDL DiscoveryGate for Academics]

  22. Sharing Instruction

  23. Problems

  24. Problems • Competition for students from established chemistry graduate programs • Lack of financial support for the students • Lack of a PhD program • What to teach in this huge field • Lack of background in the discipline on the part of the students

  25. Problem: Students with Little or No Background in Science or CS • Often MS students have good computer science background, but little or no science training or vice versa • Solution: Remedial courses • Chemical Foundation for Bioinformatics http://www.poly.edu/catalog03-05/catalog03-05-21-bioinformatics.pdf • Polytechnic University (Brooklyn) • Introduction to Genomics • Indiana University • A-level graduate courses in Computer Science • Indiana University • Dilemma: Should remedial courses count toward the MS degree?

  26. Problem: Little exposure to chemical informatics as undergrads • Can a student really master chemical informatics in a 1- or 2-year MS program?

  27. Huge Size of the Chemical Literature • ~ 50 million chemical substances • ~ 6 million reagents • ~ 7 million published reactions • ~16,000 protein crystal structures • ~250,000 small molecule x-ray structures Glen, Robert; Aldridge, Susan. “Developing tools and standards in molecular informatics.” Chemical Communications2002, (23), 2745-2747. DOI: 10.1039/b207793k http://xlink.rsc.org/?DOI=b207793k

  28. Bioinformatics

  29. IU Bioinformatics Programs • Also started in 2001 • Approximately 50 students in the program between the two campuses • Nine degrees awarded to date • Emphasis on the computer science side of the field • Recently recruited seven new faculty with research interests in bioinformatics

  30. Bioinformatics Faculty at IUB • SUN KIM • MEHMET (MEMO) DALKILIC • HAIXU TANG • ALESSANDRO FLAMMINI • ALESSANDRO VESPIGNANI • LUIS MATEUS ROCHA • SANTIAGO SCHNELL • LARRY YAEGER • PETER CHERBAS (adjunct) • JAMES GLAZIER (adjunct) • ALEXANDER BOLSHOY (visiting) • PREDRAG RADIVOJAC (visiting)

  31. Bioinformatics Faculty at IUPUI • A. KEITH DUNKER • ARIEL FERNANDEZ • JEFFREY HUANG • SNEHASIS MUKHOPADHYAY • NARAYAN PERUMAL (visiting) • MALIKA MAHOUI (visiting) • ZINA BEN-MILED (adjunct)

  32. Directories: bio1nf0rm (US only) • 64 programs listed • Degrees range from dedicated programs to specialized tracks within computer science or biology departments • 3 of the 64 began accepting students in 2003, compared to 14 in 2002 and 17 in 2001 • Over half of the programs began in the last three years!

  33. Survey: Bio1nf0rm 2003 • 44 MS programs awarded 117 degrees • 46 PhD programs awarded 35 degrees • Seven schools have all three levels of programs • Graduates: 201 in 2003, 181 in 2002, 53 in 2001 (BS, MS, or PhD) • 60% are male; 40% are female

  34. UKeU: UK eUniversities Worldwide • Established in 2001 • For students anywhere in the world • Has a global service support infrastructure - available 24x7 http://www.ukeu.com/index.php?site=

  35. UKeU MSc in Bioinformatics • University of Leeds and University of Manchester • Next start date: 4 October 2004 • Duration: 1 ½ years at part-time • Requirements: Undergraduate degree in any discipline and proficiency in English • Fee: GBP 9,000 • http://www.ukeu.com/courses/bioinformatics/courses_bioinformatics.php?site=students

  36. Indiana Initiatives • Indiana Genomics Initiative • http://www.ingen.iu.edu/ • Inproteo (Indiana Proteomics Consortium) • http://www.inproteomics.com/index.html • Bio Crossroads (Central Indiana Life Science Network) • http://www.biocrossroads.com/default.htm

  37. Indiana University’s Bioinformatics Initiatives: Indy • Center for Computational Biology and Bioinformatics at Indianapolis • http://www.compbio.iupui.edu/

  38. Indiana University’s Bioinformatics Initiatives: IUB • Center for Genomics and Bioinformatics • http://cgb.indiana.edu/ • Biocomplexity Institute • http://biocomplexity.indiana.edu/ • Proteomics Research and Development Facility • http://www.chem.indiana.edu/facilities/proteomics/PRDFhomepage.htm • Flybase Drosophila Genome Database • http://flybase.bio.indiana.edu/

  39. Future

  40. Future • Implement the PhD program in science informatics • Aggressively recruit students to both the MS and PhD programs • Recruit additional faculty • Seek additional financial support for students • Move into distance education • Forge additional partnerships with the chemical, bioscience, and pharmaceutical industries, with chemical and bioiscience informatics and other relevant software and database companies • Work closely with the newly formed Science Informatics Advisory Board

  41. School of InformaticsScience Informatics Advisory Board(as of 8/19/2004) • Esther Allen (Consultant; formerly, MDL) • Malorye Branco (Bio-IT World • Caroline Kovac (IBM Healthcare and Life Sciences) • Rudy Potenzone, Sr. (Ingenuity Systems) • Lura Powell (AIT, Advanced Imaging Technologies • John Reynders (Eli Lilly & Co.) • Richard A. Roberts (Pfizer) • Ray Salemme (Linguagen; formerly, 3DP) • Mick Savage (Consultant; formerly MSI, now Accelrys)

  42. Thanks to Graduate Fellowship Sponsors: Daylight Chemical Information Systems MDL Information Systems

  43. Bibliography • Calandra, Bob. “Bioinformatics knowledge vital to careers.” The ScientistSeptember 2, 2002, 16(17). http://www.thescientist.com/yr2002/sep/prof1_020902.html • Ham, Becky. “Bioinformatics.” ChemistryWinter 2004, 9-10.http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=Chemistry%5Cindex.html • Harmon, G.; Garfield, E.; Paris, G. et al. “Bioinformatics in information science education.” Proceedings of the ASIST Annual Meeting 2002, 39, 490-491. • Henry, Celia M. “Careers in bioinformatics.” Chemical & Engineering NewsApril 8, 2002, 80(14), 83-84, 86.

  44. Bibliography (cont’d) • Russo, Eugene. “Chemistry plans a structural overhaul.” NatureSeptember 12, 2002, 419(6903), J4-J7. DOI: http://dx.doi.org/10.1038/nj6903-04a • Schofield, Helen; Wiggins, Gary; Willett, Peter. "Recent developments in chemoinformatics education." Drug Discovery TodaySeptember 2001, 6(18), 931-934. • Toner, Bernadette. “Number of bioinformatics grads grows, but rise in degree programs slows in 2003.” bio1nf0rmAugust 11, 2003, 7(32), 1, 6-10. • Wiggins, Gary. “Teaching chemical literature, databases, and chemical informatics.” CPT; Committee on Professional Training [newsletter] Spring 2004, 4(1), 1-2. http://www.chemistry.org/portal/resources/ACS/ACSContent/education/cpt/nl_cpt_spring2004.pdf

  45. Chemical Informatics Textbooks • Leach, Andrew R.; Gillet, Valerie J. An Introduction to Chemoinformatics. Kluwer, 2003. ISBN 1-4020-1347-7 • Gasteiger,Johann;Engel, Thomas. Chemoinformatics: A Textbook. Wiley-VCH, 2003. ISBN 3-527-30681-1 • Bajorath, Jürgen, Ed. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery. (Methods in Molecular Biology; 275) Humana, 2004. ISBN 1-58829-261-4

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