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Chemical Informatics and Chemical Informatics and Bioinformatics Programs at Bioinformatics Programs at
Indiana UniversityIndiana UniversityGary WigginsGary Wiggins
School of InformaticsSchool of InformaticsIndiana UniversityIndiana University
ACS, Philadelphia, 23 August 2004ACS, Philadelphia, 23 August 2004
OverviewOverview
Comments on Chemical Informatics as a Comments on Chemical Informatics as a DisciplineDiscipline
Other Programs and CoursesOther Programs and Courses Indiana University ProgramsIndiana University ProgramsProblemsProblemsBioinformatics ProgramsBioinformatics ProgramsFutureFuture
JJüürgen Bajorath on rgen Bajorath on Chemoinformatics, etc.Chemoinformatics, etc.
Chem-, chemi-, or chemo-informaticsChem-, chemi-, or chemo-informaticsFocus on the information resources needed to Focus on the information resources needed to
optimize the properties of a ligand to become optimize the properties of a ligand to become a drug (Frank Brown, 1998)a drug (Frank Brown, 1998)Decision support by computational meansDecision support by computational meansDrug discoveryDrug discovery
Chemical Informatics: the application of Chemical Informatics: the application of information technology to chemistry (not information technology to chemistry (not with a specific focus on drug discovery)with a specific focus on drug discovery)
Related Terms per BajorathRelated Terms per Bajorath
ChemometricsChemometricsApplication of statistical methods to chemical Application of statistical methods to chemical
data and the derivation of relevant statistical data and the derivation of relevant statistical models and descriptorsmodels and descriptors
Increasingly difficult to distinguish between Increasingly difficult to distinguish between chemometrics and chemoinformaticschemometrics and chemoinformatics
Discovery informatics—acknowledges that Discovery informatics—acknowledges that gaining knowledge from chemical data gaining knowledge from chemical data alone is insufficient for success in drug alone is insufficient for success in drug discoverydiscovery
Bajorath’s ConclusionsBajorath’s Conclusions
Boundaries between bioinformatics and Boundaries between bioinformatics and chemoinformatics are fluidchemoinformatics are fluidBoth should be closely combined or merged Both should be closely combined or merged
to significantly impact biotechnology or to significantly impact biotechnology or pharmaceutical researchpharmaceutical research
Bajorath, JBajorath, Jüürgen, Ed. rgen, Ed. Chemoinformatics: Concepts, Methods, and Tools for Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery.Drug Discovery. (Methods in Molecular Biology; 275) Humana Press: (Methods in Molecular Biology; 275) Humana Press: Totawa, NJ, 2004.Totawa, NJ, 2004.
Another Program in the USAnother Program in the US
University of Massachusetts, LowellUniversity of Massachusetts, LowellMS in Computer Science with an option in MS in Computer Science with an option in
Bio/CheminformaticsBio/CheminformaticsPrescribed courses for 30 hours (assuming all Prescribed courses for 30 hours (assuming all
prerequisites met)prerequisites met)Thesis may count for 6 of the hoursThesis may count for 6 of the hoursRepesentative course: Selected topics in Repesentative course: Selected topics in
Chemistry: Protein and Chemical InformaticsChemistry: Protein and Chemical InformaticsAlso offer a Doctor of Science degreeAlso offer a Doctor of Science degreehttp://http://genome.uml.edu/programs_grad.htmgenome.uml.edu/programs_grad.htm
Selected Courses in Selected Courses in CheminformaticsCheminformatics
Introduction to Chemoinformatics Course at the Introduction to Chemoinformatics Course at the University of MichiganUniversity of Michigan Offered through the interdisciplinary program in Pharmaceutical Offered through the interdisciplinary program in Pharmaceutical
EngineeringEngineering Taught by David WildTaught by David Wild http://www-personal.engin.umich.edu/~wildd/chemoinf/http://www-personal.engin.umich.edu/~wildd/chemoinf/
index.htmlindex.html Chemoinformatics Course at The Danish University of Chemoinformatics Course at The Danish University of
Pharmaceutical SciencesPharmaceutical Scienceshttp://www.dfh.dk/phd/courses/descriptions/courses20042005/http://www.dfh.dk/phd/courses/descriptions/courses20042005/
chemoinformatics.htmchemoinformatics.htm Analytical Informatics at Purdue (Randy Julian)Analytical Informatics at Purdue (Randy Julian)
http://http://miner.chem.purdue.eduminer.chem.purdue.edu//
Bogus Programs???Bogus Programs???
Institute of Cheminformatics StudiesInstitute of Cheminformatics Studies
http://www.cheminformaticscentre.org/chem/http://www.cheminformaticscentre.org/chem/ NC State University Certified Bioinformatics NC State University Certified Bioinformatics
Specialist: CheminformaticsSpecialist: Cheminformatics
http://www.ncsu.edu/ctu/documents/pdfdocs/markhttp://www.ncsu.edu/ctu/documents/pdfdocs/marketingpackets/biochembrochure.pdfetingpackets/biochembrochure.pdf Chemoinformatics National BioInformatics Chemoinformatics National BioInformatics
InstituteInstitute
http://www.bioinfoinstitute.com/chemoinfo.htmhttp://www.bioinfoinstitute.com/chemoinfo.htm
Indiana University Programs in Indiana University Programs in Chemical InformaticsChemical Informatics
Specialized Chemistry Degree Options Specialized Chemistry Degree Options at Indiana Universityat Indiana University
BS in Informatics with a chemistry or biology BS in Informatics with a chemistry or biology cognate (essentially a minor)cognate (essentially a minor)
MS in Chemical InformaticsMS in Chemical Informatics MS in BioinformaticsMS in Bioinformatics PhD in Science Informatics (expected Fall 2005)PhD in Science Informatics (expected Fall 2005)http://http://www.informatics.indiana.eduwww.informatics.indiana.edu
MLS or MIS with a specialization in chemical MLS or MIS with a specialization in chemical informationinformation
http://www.slis.indiana.eduhttp://www.slis.indiana.edu
IU’s MS in Chemical InformaticsIU’s MS in Chemical Informatics
Developed jointly by the School of Developed jointly by the School of Informatics and chemistry departments at Informatics and chemistry departments at IUB and IUPUIIUB and IUPUI
First students admitted at IUPUI in fall First students admitted at IUPUI in fall 2001 and at IUB in fall 20022001 and at IUB in fall 2002
Graduates: 4Graduates: 4Currently enrolled: 11Currently enrolled: 11
Unique Program at IUPUIUnique Program at IUPUI
Laboratory Informatics track at IUPUILaboratory Informatics track at IUPUI Instrumentation and data interfacingInstrumentation and data interfacingLaboratory notebooksLaboratory notebooksLaboratory Information Management Systems Laboratory Information Management Systems
(LIMS)(LIMS)
Why IU for Chemical Informatics?Why IU for Chemical Informatics?
Outstanding FacultyOutstanding Faculty Excellent computer facilities and infrastructureExcellent computer facilities and infrastructure Close proximity to major pharmaceutical Close proximity to major pharmaceutical
companies (Lilly, Abbott, Pfizer) and to chemical companies (Lilly, Abbott, Pfizer) and to chemical informatics companies (Tripos, LeadScope, informatics companies (Tripos, LeadScope, Chemical Abstracts Service)Chemical Abstracts Service)
History of innovative, IT-based chemical History of innovative, IT-based chemical information services (QCPE, MSC)information services (QCPE, MSC)
Well-established programs in IU’s SLISWell-established programs in IU’s SLIS
Core and Affilated Faculty at IUBCore and Affilated Faculty at IUB
MU-HYUN (MOOKIE) BAIKMU-HYUN (MOOKIE) BAIK SANTIAGO SCHNELLSANTIAGO SCHNELL DAVID WILDDAVID WILD (visiting) (visiting) DIMITRIS AGRAFIOTIS DIMITRIS AGRAFIOTIS (adjunct)(adjunct) JOHN BARNARD JOHN BARNARD (adjunct)(adjunct) JOHN C. HUFFMANJOHN C. HUFFMAN (adjunct) (adjunct) GEORGE W. A. MILNE GEORGE W. A. MILNE (adjunct)(adjunct) PETER ORTOLEVA PETER ORTOLEVA (adjunct)(adjunct) GARY WIGGINSGARY WIGGINS (adjunct) (adjunct) KEVIN GILBERTKEVIN GILBERT (affiliated) (affiliated) CHARLES H. DAVISCHARLES H. DAVIS (affiliated) (affiliated)
Core and Affilated Faculty at IUPUICore and Affilated Faculty at IUPUI
SAM A.F. MILOSEVICHSAM A.F. MILOSEVICHMAHESH MERCHANTMAHESH MERCHANTJOHN MCKELVEYJOHN MCKELVEY (adjunct) (adjunct)DON BOYDDON BOYD (affiliated) (affiliated)KELSEY FORSYTHEKELSEY FORSYTHE (affiliated) (affiliated)
Outreach ActivitiesOutreach Activities
Research relationships withResearch relationships with IU School of MedicineIU School of Medicine IUB/IUPUI bioinformatics and proteomics IUB/IUPUI bioinformatics and proteomics
research programsresearch programsCommercial firms through internships Commercial firms through internships
(LeadScope, Rosetta Inpharmatics, Lilly)(LeadScope, Rosetta Inpharmatics, Lilly)
IU Undergraduate CoursesIU Undergraduate Courses
Four one-credit undergrad coursesFour one-credit undergrad coursesC371 Chemical Informatics IC371 Chemical Informatics IC372 Chemical Informatics II: Molecular C372 Chemical Informatics II: Molecular
ModelingModelingC471 Chemical Information Sources and C471 Chemical Information Sources and
ServicesServicesC472 Computer Sources for Chemical C472 Computer Sources for Chemical
InformationInformation
IU Graduate CoursesIU Graduate Courses
Two three-credit graduate coursesTwo three-credit graduate coursesC571 Chemical Information TechnologyC571 Chemical Information TechnologyC572 Molecular Modeling & Computational C572 Molecular Modeling & Computational
ChemistryChemistryNew courses under developmentNew courses under development
Programming for Chemical InformaticsProgramming for Chemical Informatics Information Retrieval from Chemistry and Life Information Retrieval from Chemistry and Life
Sciences DatabasesSciences Databases
Tools Used or Planned for UseTools Used or Planned for Use SpotfireSpotfire ChemTK LiteChemTK Lite Chemaxon’s MarvinChemaxon’s Marvin Chemical Computing Group’s MOEChemical Computing Group’s MOE Daylight ToolkitDaylight Toolkit OpenEye (all modules)OpenEye (all modules) BCI softwareBCI software WaveFunction’s SpartanWaveFunction’s Spartan Serena Software’s PCModelSerena Software’s PCModel [MDL DiscoveryGate for Academics][MDL DiscoveryGate for Academics]
ProblemsProblems
Competition for students from established Competition for students from established chemistry graduate programschemistry graduate programs
Lack of financial support for the studentsLack of financial support for the studentsLack of a PhD programLack of a PhD programWhat to teach in this huge fieldWhat to teach in this huge fieldLack of background in the discipline on the Lack of background in the discipline on the
part of the studentspart of the students
Problem: Students with Little or No Problem: Students with Little or No Background in Science or CSBackground in Science or CS
Often MS students have good computer science Often MS students have good computer science background, but little or no science training or vice versabackground, but little or no science training or vice versa
Solution: Remedial coursesSolution: Remedial courses Chemical Foundation for BioinformaticsChemical Foundation for Bioinformatics
http://www.poly.edu/catalog03-05/catalog03-05-21-bioinformatics.pdfhttp://www.poly.edu/catalog03-05/catalog03-05-21-bioinformatics.pdf Polytechnic University (Brooklyn)Polytechnic University (Brooklyn)
Introduction to GenomicsIntroduction to Genomics Indiana UniversityIndiana University
A-level graduate courses in Computer ScienceA-level graduate courses in Computer Science Indiana UniversityIndiana University
Dilemma: Should remedial courses count toward the MS Dilemma: Should remedial courses count toward the MS degree?degree?
Problem: Little exposure to Problem: Little exposure to chemical informatics as undergradschemical informatics as undergradsCan a student really master chemical Can a student really master chemical
informatics in a 1- or 2-year MS program?informatics in a 1- or 2-year MS program?
Huge Size of the Chemical Huge Size of the Chemical LiteratureLiterature
~ 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 Glen, Robert; Aldridge, Susan. “Developing tools and standards in molecular informatics.” informatics.” Chemical CommunicationsChemical Communications 20022002, , (23),(23), 2745-2747. DOI: 2745-2747. DOI: 10.1039/b207793k10.1039/b207793khttp://http://xlink.rsc.orgxlink.rsc.org/?DOI=b207793k/?DOI=b207793k
IU Bioinformatics ProgramsIU Bioinformatics Programs
Also started in 2001Also started in 2001Approximately 50 students in the program Approximately 50 students in the program
between the two campusesbetween the two campusesNine degrees awarded to dateNine degrees awarded to dateEmphasis on the computer science side of Emphasis on the computer science side of
the fieldthe fieldRecently recruited seven new faculty with Recently recruited seven new faculty with
research interests in bioinformaticsresearch interests in bioinformatics
Bioinformatics Faculty at IUBBioinformatics Faculty at IUB SUN KIMSUN KIM MEHMET (MEMO) DALKILICMEHMET (MEMO) DALKILIC HAIXU TANGHAIXU TANG ALESSANDRO FLAMMINIALESSANDRO FLAMMINI ALESSANDRO VESPIGNANIALESSANDRO VESPIGNANI LUIS MATEUS ROCHALUIS MATEUS ROCHA SANTIAGO SCHNELLSANTIAGO SCHNELL LARRY YAEGERLARRY YAEGER PETER CHERBASPETER CHERBAS (adjunct) (adjunct) JAMES GLAZIERJAMES GLAZIER (adjunct) (adjunct) ALEXANDER BOLSHOYALEXANDER BOLSHOY (visiting) (visiting) PREDRAG RADIVOJACPREDRAG RADIVOJAC (visiting) (visiting)
Bioinformatics Faculty at IUPUIBioinformatics Faculty at IUPUI
A. KEITH DUNKERA. KEITH DUNKERARIEL FERNANDEZARIEL FERNANDEZJEFFREY HUANGJEFFREY HUANGSNEHASIS MUKHOPADHYAYSNEHASIS MUKHOPADHYAYNARAYAN PERUMALNARAYAN PERUMAL (visiting) (visiting)MALIKA MAHOUIMALIKA MAHOUI (visiting) (visiting)ZINA BEN-MILEDZINA BEN-MILED (adjunct) (adjunct)
Directories: bio1nf0rm Directories: bio1nf0rm (US only)(US only)
64 programs listed64 programs listed Degrees range from dedicated programs to Degrees range from dedicated programs to
specialized tracks within computer science or specialized tracks within computer science or biology departments biology departments
3 of the 64 began accepting students in 2003, 3 of the 64 began accepting students in 2003, compared to 14 in 2002 and 17 in 2001compared to 14 in 2002 and 17 in 2001 Over half of the programs began in the last three Over half of the programs began in the last three
years!years!
Survey: Bio1nf0rm 2003Survey: Bio1nf0rm 2003
44 MS programs awarded 117 degrees44 MS programs awarded 117 degrees46 PhD programs awarded 35 degrees46 PhD programs awarded 35 degreesSeven schools have all three levels of Seven schools have all three levels of
programsprogramsGraduates: 201 in 2003, 181 in 2002, 53 in Graduates: 201 in 2003, 181 in 2002, 53 in
2001 (BS, MS, or PhD)2001 (BS, MS, or PhD)60% are male; 40% are female60% are male; 40% are female
UKeU: UK eUniversities WorldwideUKeU: UK eUniversities Worldwide
Established in 2001Established in 2001For students anywhere in the worldFor students anywhere in the worldHas a global service support Has a global service support
infrastructure - available 24x7 infrastructure - available 24x7 http://www.ukeu.com/index.php?site=http://www.ukeu.com/index.php?site=
UKeU MSc in BioinformaticsUKeU MSc in Bioinformatics
University of Leeds and University of University of Leeds and University of ManchesterManchester
Next start date: 4 October 2004Next start date: 4 October 2004Duration: 1 ½ years at part-timeDuration: 1 ½ years at part-timeRequirements: Undergraduate degree in Requirements: Undergraduate degree in
any discipline and proficiency in Englishany discipline and proficiency in EnglishFee: GBP 9,000Fee: GBP 9,000 http://www.ukeu.com/courses/bioinformatics/courses_bioinformatics.php?site=studentshttp://www.ukeu.com/courses/bioinformatics/courses_bioinformatics.php?site=students
Indiana InitiativesIndiana Initiatives
Indiana Genomics InitiativeIndiana Genomics Initiativehttp://www.ingen.iu.edu/http://www.ingen.iu.edu/
Inproteo (Indiana Proteomics Consortium)Inproteo (Indiana Proteomics Consortium)http://www.inproteomics.com/index.htmlhttp://www.inproteomics.com/index.html
Bio Crossroads (Central Indiana Life Bio Crossroads (Central Indiana Life Science Network)Science Network)http://www.biocrossroads.com/default.htmhttp://www.biocrossroads.com/default.htm
Indiana University’s Indiana University’s Bioinformatics Initiatives: IndyBioinformatics Initiatives: Indy
Center for Computational Biology and Center for Computational Biology and Bioinformatics at IndianapolisBioinformatics at Indianapolis
http://www.compbio.iupui.edu/http://www.compbio.iupui.edu/
Indiana University’s Indiana University’s Bioinformatics Initiatives: IUBBioinformatics Initiatives: IUB
Center for Genomics and BioinformaticsCenter for Genomics and Bioinformatics http://cgb.indiana.edu/http://cgb.indiana.edu/
Biocomplexity InstituteBiocomplexity Institute http://biocomplexity.indiana.edu/http://biocomplexity.indiana.edu/
Proteomics Research and Development FacilityProteomics Research and Development Facility http://www.chem.indiana.edu/facilities/proteomics/http://www.chem.indiana.edu/facilities/proteomics/
PRDFhomepage.htmPRDFhomepage.htm Flybase Drosophila Genome DatabaseFlybase Drosophila Genome Database
http://flybase.bio.indiana.edu/http://flybase.bio.indiana.edu/
FutureFuture Implement the PhD program in science informaticsImplement the PhD program in science informatics Aggressively recruit students to both the MS and PhD Aggressively recruit students to both the MS and PhD
programsprograms Recruit additional facultyRecruit additional faculty Seek additional financial support for studentsSeek additional financial support for students Move into distance educationMove into distance education Forge additional partnerships with the chemical, Forge additional partnerships with the chemical,
bioscience, and pharmaceutical industries, with chemical bioscience, and pharmaceutical industries, with chemical and bioiscience informatics and other relevant software and bioiscience informatics and other relevant software and database companiesand database companies
Work closely with the newly formed Science Informatics Work closely with the newly formed Science Informatics Advisory BoardAdvisory Board
School of InformaticsSchool of InformaticsScience Informatics Advisory BoardScience Informatics Advisory Board
(as of 8/19/2004)(as of 8/19/2004)
Esther Allen (Consultant; formerly, MDL)Esther Allen (Consultant; formerly, MDL) Malorye Branco (Bio-IT WorldMalorye 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 TechnologiesLura 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)
Thanks to Graduate Fellowship Thanks to Graduate Fellowship Sponsors:Sponsors:
Daylight Chemical Information SystemsDaylight Chemical Information Systems
MDL Information SystemsMDL Information Systems
BibliographyBibliography Calandra, Bob. “Bioinformatics knowledge vital to Calandra, Bob. “Bioinformatics knowledge vital to
careers.” careers.” The ScientistThe Scientist September 2, 2002September 2, 2002, 16(17). , 16(17). http://www.thescientist.com/yr2002/sep/prof1_020902.hthttp://www.thescientist.com/yr2002/sep/prof1_020902.htmlml
Ham, Becky. “Bioinformatics.” Ham, Becky. “Bioinformatics.” ChemistryChemistry Winter 2004Winter 2004, , 9-10.9-10. http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=Chemistry%5Cindex.htmlDOC=Chemistry%5Cindex.html
Harmon, G.; Garfield, E.; Paris, G. et al.Harmon, G.; Garfield, E.; Paris, G. et al. “ “Bioinformatics Bioinformatics in information science education.” Proceedings of the in information science education.” Proceedings of the ASIST Annual Meeting ASIST Annual Meeting 20022002, , 3939, 490-491., 490-491.
Henry, Celia M. “Careers in bioinformatics.” Henry, Celia M. “Careers in bioinformatics.” Chemical & Chemical & Engineering NewsEngineering News April 8, 2002April 8, 2002, , 80(14),80(14), 83-84, 86. 83-84, 86.
Bibliography (cont’d)Bibliography (cont’d) Russo, Eugene. “Chemistry plans a structural overhaul.” Russo, Eugene. “Chemistry plans a structural overhaul.”
NatureNature September 12, 2002September 12, 2002, , 419(6903), 419(6903), J4-J7. DOI: J4-J7. DOI: http://dx.doi.org/10.1038/nj6903-04ahttp://dx.doi.org/10.1038/nj6903-04a
Schofield, Helen; Wiggins, Gary; Willett, Peter. "Recent Schofield, Helen; Wiggins, Gary; Willett, Peter. "Recent developments in chemoinformatics education." developments in chemoinformatics education." Drug Drug Discovery TodayDiscovery Today September 2001September 2001, , 6(18),6(18), 931-934. 931-934.
Toner, Bernadette. “Number of bioinformatics grads Toner, Bernadette. “Number of bioinformatics grads grows, but rise in degree programs slows in 2003.” grows, but rise in degree programs slows in 2003.” bio1nf0rmbio1nf0rm August 11, 2003August 11, 2003, , 7(32),7(32), 1, 6-10. 1, 6-10.
Wiggins, Gary. “Teaching chemical literature, databases, Wiggins, Gary. “Teaching chemical literature, databases, and chemical informatics.” CPT; Committee on and chemical informatics.” CPT; Committee on Professional Training [newsletter] Professional Training [newsletter] Spring 2004Spring 2004, , 4(1),4(1), 1-2. 1-2.http://www.chemistry.org/portal/resources/ACS/http://www.chemistry.org/portal/resources/ACS/
ACSContent/education/cpt/nl_cpt_spring2004.pdfACSContent/education/cpt/nl_cpt_spring2004.pdf
Chemical Informatics TextbooksChemical Informatics Textbooks
Leach, Andrew R.; Gillet, Valerie J. An Leach, Andrew R.; Gillet, Valerie J. An Introduction to Chemoinformatics. Kluwer, 2003. Introduction to Chemoinformatics. Kluwer, 2003. ISBN 1-4020-1347-7 ISBN 1-4020-1347-7
Gasteiger,Johann;Engel, Thomas. Gasteiger,Johann;Engel, Thomas. Chemoinformatics: A Textbook. Wiley-VCH, Chemoinformatics: A Textbook. Wiley-VCH, 2003. ISBN 3-527-30681-12003. ISBN 3-527-30681-1
Bajorath, JBajorath, Jürgen, Ed. ürgen, Ed. Chemoinformatics: Chemoinformatics: Concepts, Methods, and Tools for Drug Concepts, Methods, and Tools for Drug Discovery.Discovery. (Methods in Molecular Biology; 275) (Methods in Molecular Biology; 275) Humana, 2004. ISBN 1-58829-261-4Humana, 2004. ISBN 1-58829-261-4