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

3. Comments on Chemical Informatics as a Discipline

4. Jürgen Bajorath on Chemoinformatics, etc. Chem-, chemi-, or chemo-informatics 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) 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 Decision support by computational means Drug discovery Drug discovery Chemical Informatics: the application of information technology to chemistry (not with a specific focus on 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 Chemometrics Application of statistical methods to chemical data and the derivation of relevant statistical models and descriptors Application of statistical methods to chemical data and the derivation of relevant statistical models and descriptors Increasingly difficult to distinguish between chemometrics and chemoinformatics 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 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 Boundaries between bioinformatics and chemoinformatics are fluid Both should be closely combined or merged to significantly impact biotechnology or pharmaceutical research 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 University of Massachusetts, Lowell MS in Computer Science with an option in Bio/Cheminformatics MS in Computer Science with an option in Bio/Cheminformatics Prescribed courses for 30 hours (assuming all prerequisites met) Prescribed courses for 30 hours (assuming all prerequisites met) Thesis may count for 6 of the hours Thesis may count for 6 of the hours Repesentative course: Selected topics in Chemistry: Protein and Chemical Informatics Repesentative course: Selected topics in Chemistry: Protein and Chemical Informatics Also offer a Doctor of Science degree Also offer a Doctor of Science degree http://genome.uml.edu/programs_grad.htm http://genome.uml.edu/programs_grad.htm http://genome.uml.edu/programs_grad.htm

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

10. Bogus Programs??? Institute of Cheminformatics Studies Institute of Cheminformatics Studies http://www.cheminformaticscentre.org/chem/ NC State University Certified Bioinformatics Specialist: Cheminformatics NC State University Certified Bioinformatics Specialist: Cheminformatics http://www.ncsu.edu/ctu/documents/pdfdocs/mark etingpackets/biochembrochure.pdf http://www.ncsu.edu/ctu/documents/pdfdocs/mark etingpackets/biochembrochure.pdf Chemoinformatics National BioInformatics Institute 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) BS in Informatics with a chemistry or biology cognate (essentially a minor) MS in Chemical Informatics MS in Chemical Informatics MS in Bioinformatics MS in Bioinformatics PhD in Science Informatics (expected Fall 2005) PhD in Science Informatics (expected Fall 2005) http://www.informatics.indiana.edu MLS or MIS with a specialization in chemical information 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 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 First students admitted at IUPUI in fall 2001 and at IUB in fall 2002 Graduates: 4 Graduates: 4 Currently enrolled: 11 Currently enrolled: 11

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

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

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

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

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

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

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

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

22. Sharing Instruction

23. Problems

24. Problems Competition for students from established chemistry graduate programs Competition for students from established chemistry graduate programs Lack of financial support for the students Lack of financial support for the students Lack of a PhD program Lack of a PhD program What to teach in this huge field What to teach in this huge field Lack of background in the discipline on the part of the students 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 Often MS students have good computer science background, but little or no science training or vice versa Solution: Remedial courses Solution: Remedial courses Chemical Foundation for Bioinformatics Chemical Foundation for Bioinformatics http://www.poly.edu/catalog03-05/catalog03-05-21-bioinformatics.pdf Polytechnic University (Brooklyn) Polytechnic University (Brooklyn) Introduction to Genomics Introduction to Genomics Indiana University Indiana University A-level graduate courses in Computer Science A-level graduate courses in Computer Science Indiana University Indiana University Dilemma: Should remedial courses count toward the MS degree? 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? 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 ~ 50 million chemical substances ~ 6 million reagents ~ 6 million reagents ~ 7 million published reactions ~ 7 million published reactions ~16,000 protein crystal structures ~16,000 protein crystal structures ~250,000 small molecule x-ray structures ~250,000 small molecule x-ray structures Glen, Robert; Aldridge, Susan. “Developing tools and standards in molecular informatics.” Chemical Communications 2002, (23), 2745-2747. DOI: 10.1039/b207793k http://xlink.rsc.org/?DOI=b207793k

28. Bioinformatics

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

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

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

32. Directories: bio1nf0rm (US only) 64 programs listed 64 programs listed Degrees range from dedicated programs to specialized tracks within computer science or biology departments 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 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! Over half of the programs began in the last three years!

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

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

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

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

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

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

39. Future

40. Future Implement the PhD program in science informatics Implement the PhD program in science informatics Aggressively recruit students to both the MS and PhD programs Aggressively recruit students to both the MS and PhD programs Recruit additional faculty Recruit additional faculty Seek additional financial support for students Seek additional financial support for students Move into distance education 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 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 Work closely with the newly formed Science Informatics Advisory Board

41. School of Informatics Science Informatics Advisory Board (as of 8/19/2004) Esther Allen (Consultant; formerly, MDL) Esther Allen (Consultant; formerly, MDL) Malorye Branco (Bio-IT World Malorye Branco (Bio-IT World Caroline Kovac (IBM Healthcare and Life Sciences) Caroline Kovac (IBM Healthcare and Life Sciences) Rudy Potenzone, Sr. (Ingenuity Systems) Rudy Potenzone, Sr. (Ingenuity Systems) Lura Powell (AIT, Advanced Imaging Technologies Lura Powell (AIT, Advanced Imaging Technologies John Reynders (Eli Lilly & Co.) John Reynders (Eli Lilly & Co.) Richard A. Roberts (Pfizer) Richard A. Roberts (Pfizer) Ray Salemme (Linguagen; formerly, 3DP) Ray Salemme (Linguagen; formerly, 3DP) Mick Savage (Consultant; formerly MSI, now Accelrys) 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 Scientist September 2, 2002, 16(17). http://www.thescientist.com/yr2002/sep/prof1_020902.ht ml Calandra, Bob. “Bioinformatics knowledge vital to careers.” The Scientist September 2, 2002, 16(17). http://www.thescientist.com/yr2002/sep/prof1_020902.ht ml http://www.thescientist.com/yr2002/sep/prof1_020902.ht ml http://www.thescientist.com/yr2002/sep/prof1_020902.ht ml Ham, Becky. “Bioinformatics.” Chemistry Winter 2004, 9-10. http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html? DOC=Chemistry%5Cindex.html Ham, Becky. “Bioinformatics.” Chemistry Winter 2004, 9-10. http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html? DOC=Chemistry%5Cindex.html http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html? DOC=Chemistry%5Cindex.html 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. 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 News April 8, 2002, 80(14), 83-84, 86. Henry, Celia M. “Careers in bioinformatics.” Chemical & Engineering News April 8, 2002, 80(14), 83-84, 86.

44. Bibliography (cont’d) Russo, Eugene. “Chemistry plans a structural overhaul.” Nature September 12, 2002, 419(6903), J4-J7. DOI: http://dx.doi.org/10.1038/nj6903-04a Russo, Eugene. “Chemistry plans a structural overhaul.” Nature September 12, 2002, 419(6903), J4-J7. DOI: http://dx.doi.org/10.1038/nj6903-04a http://dx.doi.org/10.1038/nj6903-04a Schofield, Helen; Wiggins, Gary; Willett, Peter. "Recent developments in chemoinformatics education." Drug Discovery Today September 2001, 6(18), 931-934. Schofield, Helen; Wiggins, Gary; Willett, Peter. "Recent developments in chemoinformatics education." Drug Discovery Today September 2001, 6(18), 931-934. Toner, Bernadette. “Number of bioinformatics grads grows, but rise in degree programs slows in 2003.” bio1nf0rm August 11, 2003, 7(32), 1, 6-10. Toner, Bernadette. “Number of bioinformatics grads grows, but rise in degree programs slows in 2003.” bio1nf0rm August 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. 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/ACSCo ntent/education/cpt/nl_cpt_spring2004.pdf http://www.chemistry.org/portal/resources/ACS/ACSCo ntent/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 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 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 Bajorath, Jürgen, Ed. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery. (Methods in Molecular Biology; 275) Humana, 2004. ISBN 1-58829-261-4