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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 DisciplineDisciplineOther Programs and CoursesOther Programs and CoursesIndiana University ProgramsIndiana University ProgramsProblemsProblemsBioinformatics ProgramsBioinformatics ProgramsFutureFuture

Comments on Chemical Comments on Chemical Informatics as a DisciplineInformatics as a Discipline

JJüürgenrgen BajorathBajorath on on ChemoinformaticsChemoinformatics, etc., etc.

ChemChem--, , chemichemi--, or chemo, or chemo--informaticsinformaticsFocus on the information resources needed to Focus on the information resources needed to optimize the properties of a optimize the properties of a ligandligand to become 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 Related Terms per BajorathBajorath

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 descriptorsIncreasingly difficult to distinguish between Increasingly difficult to distinguish between chemometricschemometrics and and chemoinformaticschemoinformatics

Discovery informaticsDiscovery informatics——acknowledges that 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’sBajorath’s ConclusionsConclusions

Boundaries between bioinformatics and Boundaries between bioinformatics and chemoinformaticschemoinformatics are fluidare fluid

Both 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

BajorathBajorath, , JJüürgenrgen, Ed. , Ed. ChemoinformaticsChemoinformatics: Concepts, Methods, and Tools for : Concepts, Methods, and Tools for Drug Discovery.Drug Discovery. (Methods in Molecular Biology; 275) Humana Press: (Methods in Molecular Biology; 275) Humana Press: TotawaTotawa, NJ, 2004., NJ, 2004.

Other Programs and CoursesOther Programs and Courses

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/Bio/CheminformaticsCheminformaticsPrescribed 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 hoursRepesentativeRepesentative course: Selected topics in 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://genome.http://genome.umluml..eduedu/programs_grad./programs_grad.htmhtm

Selected Courses in Selected Courses in CheminformaticsCheminformatics

Introduction to Introduction to ChemoinformaticsChemoinformatics Course at the Course at the University of MichiganUniversity of Michigan

Offered through the interdisciplinary program in Pharmaceutical Offered through the interdisciplinary program in Pharmaceutical EngineeringEngineeringTaught by David WildTaught by David Wildhttp://wwwhttp://www--personal.engin.umich.edu/~wildd/chemoinf/index.htmlpersonal.engin.umich.edu/~wildd/chemoinf/index.html

ChemoinformaticsChemoinformatics Course at The Danish University of Course at The Danish University of Pharmaceutical SciencesPharmaceutical Sciences

http://www.dfh.dk/phd/courses/descriptions/courses20042005/chemohttp://www.dfh.dk/phd/courses/descriptions/courses20042005/chemoinfinformatics.htmormatics.htmAnalytical Informatics at Purdue (Randy Julian)Analytical Informatics at Purdue (Randy Julian)http://miner.chem.http://miner.chem.purduepurdue..eduedu//

Bogus Programs???Bogus Programs???

Institute of Institute of CheminformaticsCheminformatics StudiesStudieshttp://www.cheminformaticscentre.org/chem/http://www.cheminformaticscentre.org/chem/

NC State University Certified Bioinformatics NC State University Certified Bioinformatics Specialist: Specialist: CheminformaticsCheminformatics

http://www.ncsu.edu/ctu/documents/pdfdocs/markhttp://www.ncsu.edu/ctu/documents/pdfdocs/marketingpackets/biochembrochure.pdfetingpackets/biochembrochure.pdfChemoinformaticsChemoinformatics National National BioInformaticsBioInformaticsInstituteInstitute

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 InformaticsMS in BioinformaticsMS in BioinformaticsPhD in Science Informatics (expected Fall 2005)PhD in Science Informatics (expected Fall 2005)

http://www.informatics.http://www.informatics.indianaindiana..eduedu

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’sIU’s MS in Chemical InformaticsMS 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 IUPUIFirst 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 2002Graduates: 4Graduates: 4Currently enrolled: 11Currently enrolled: 11

Unique Program at IUPUIUnique Program at IUPUI

Laboratory Informatics track at IUPUILaboratory Informatics track at IUPUIInstrumentation 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 FacultyExcellent computer facilities and infrastructureExcellent computer facilities and infrastructureClose 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 (informatics companies (TriposTripos, , LeadScopeLeadScope, , Chemical Abstracts Service)Chemical Abstracts Service)History of innovative, ITHistory of innovative, IT--based chemical based chemical information services (QCPE, MSC)information services (QCPE, MSC)WellWell--established programs in established programs in IU’sIU’s SLISSLIS

Core and Core and AffilatedAffilated Faculty at IUBFaculty at IUB

MUMU--HYUN (MOOKIE) BAIKHYUN (MOOKIE) BAIKSANTIAGO SCHNELLSANTIAGO SCHNELLDAVID 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 Core and AffilatedAffilated Faculty at IUPUIFaculty 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 withIU School of MedicineIU School of MedicineIUB/IUPUI bioinformatics and proteomics IUB/IUPUI bioinformatics and proteomics research programsresearch programsCommercial firms through internships Commercial firms through internships ((LeadScopeLeadScope, Rosetta , Rosetta InpharmaticsInpharmatics, Lilly), Lilly)

IU Undergraduate CoursesIU Undergraduate Courses

Four oneFour one--credit undergrad coursescredit 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 threeTwo three--credit graduate coursescredit graduate coursesC571 Chemical Information TechnologyC571 Chemical Information TechnologyC572 Molecular Modeling & Computational C572 Molecular Modeling & Computational ChemistryChemistry

New courses under developmentNew courses under developmentProgramming for Chemical InformaticsProgramming for Chemical InformaticsInformation Retrieval from Chemistry and Life Information Retrieval from Chemistry and Life Sciences DatabasesSciences Databases

Sharing InstructionSharing Instruction

Tools Used or Planned for UseTools Used or Planned for UseSpotfireSpotfireChemTKChemTK LiteLiteChemaxon’sChemaxon’s MarvinMarvinChemical Computing Group’s MOEChemical Computing Group’s MOEDaylight ToolkitDaylight ToolkitOpenEyeOpenEye (all modules)(all modules)BCI softwareBCI softwareWaveFunction’sWaveFunction’s SpartanSpartanSerena Software’s Serena Software’s PCModelPCModel[MDL [MDL DiscoveryGateDiscoveryGate for Academics]for Academics]

ProblemsProblems

ProblemsProblems

Competition for students from established Competition for students from established chemistry graduate programschemistry graduate programsLack of a PhD programLack of a PhD programLittle financial support for the studentsLittle financial support for the studentsLack of background in the discipline on the Lack of background in the discipline on the part of the studentspart of the students

What is chemical informatics?What is chemical informatics?What to teach in this huge field?What to teach in this huge field?

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 versaSolution: Remedial coursesSolution: Remedial courses

Chemical Foundation for BioinformaticsChemical Foundation for Bioinformaticshttp://www.poly.edu/catalog03http://www.poly.edu/catalog03--05/catalog0305/catalog03--0505--2121--bioinformatics.pdfbioinformatics.pdf

Polytechnic University (Brooklyn)Polytechnic University (Brooklyn)Introduction to GenomicsIntroduction to Genomics

Indiana UniversityIndiana UniversityAA--level graduate courses in Computer Sciencelevel 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?

BioinformaticsBioinformatics

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 IUBSUN KIMSUN KIMMEHMET (MEMO) DALKILICMEHMET (MEMO) DALKILICHAIXU TANGHAIXU TANGALESSANDRO FLAMMINIALESSANDRO FLAMMINIALESSANDRO VESPIGNANIALESSANDRO VESPIGNANILUIS MATEUS ROCHALUIS MATEUS ROCHASANTIAGO SCHNELLSANTIAGO SCHNELLLARRY YAEGERLARRY YAEGERPETER 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 BENZINA BEN--MILEDMILED (adjunct)(adjunct)

Directories: bio1nf0rm Directories: bio1nf0rm (US only)(US only)

64 programs listed64 programs listedDegrees 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

UKeUUKeU: UK : UK eUniversitieseUniversities WorldwideWorldwide

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 infrastructure -- available 24x7 available 24x7

http://www.ukeu.com/index.php?sitehttp://www.ukeu.com/index.php?site==

UKeUUKeU MScMSc in Bioinformaticsin Bioinformatics

University of Leeds and University of University of Leeds and University of ManchesterManchesterNext start date: 4 October 2004Next start date: 4 October 2004Duration: 1 ½ years at partDuration: 1 ½ years at part--timetimeRequirements: Undergraduate degree in Requirements: Undergraduate degree in any discipline and proficiency in Englishany discipline and proficiency in EnglishFee: GBP 9,000Fee: GBP 9,000http://www.ukeu.com/courses/bioinformatics/courses_bioinformatichttp://www.ukeu.com/courses/bioinformatics/courses_bioinformatics.php?site=studentss.php?site=students

Indiana InitiativesIndiana Initiatives

Indiana Genomics InitiativeIndiana Genomics Initiativehttp://www.ingen.iu.edu/http://www.ingen.iu.edu/

InproteoInproteo (Indiana Proteomics Consortium)(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.http://www.biocrossroadsbiocrossroads.com/default..com/default.htmhtm

Indiana University’s Indiana University’s Bioinformatics Initiatives: IndyBioinformatics Initiatives: IndyCenter for Computational Biology and Center for Computational Biology and Bioinformatics at IndianapolisBioinformatics at Indianapolishttp://www.compbio.iupui.edu/http://www.compbio.iupui.edu/

Indiana University’s Indiana University’s Bioinformatics Initiatives: IUBBioinformatics Initiatives: IUBCenter for Genomics and BioinformaticsCenter for Genomics and Bioinformatics

http://cgb.indiana.edu/http://cgb.indiana.edu/BiocomplexityBiocomplexity InstituteInstitute

http://biocomplexity.indiana.edu/http://biocomplexity.indiana.edu/Proteomics Research and Development FacilityProteomics Research and Development Facility

http://www.chem.indiana.edu/facilities/proteomics/PRhttp://www.chem.indiana.edu/facilities/proteomics/PRDFhomepage.htmDFhomepage.htm

FlybaseFlybase Drosophila Genome DatabaseDrosophila Genome Databasehttp://flybase.bio.indiana.edu/http://flybase.bio.indiana.edu/

FutureFuture

FutureFutureImplement the PhD program in science informaticsImplement the PhD program in science informaticsAggressively recruit students to both the MS and PhD Aggressively recruit students to both the MS and PhD programsprogramsRecruit additional facultyRecruit additional facultySeek additional financial support for studentsSeek additional financial support for studentsMove into distance educationMove into distance educationForge additional partnerships with the chemical, Forge additional partnerships with the chemical, bioscience, and pharmaceutical industries, with chemical bioscience, and pharmaceutical industries, with chemical and and bioisciencebioiscience informatics and other relevant software informatics and other relevant software and database companiesand database companiesWork 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 Esther Allen (Consultant; formerly, (Consultant; formerly, MDLMDL))

Caroline Caroline KovacKovac ((IBMIBM Healthcare and Life Sciences)Healthcare and Life Sciences)

Rudy Potenzone, Sr. Rudy Potenzone, Sr. ((IngenuityIngenuity Systems)Systems)

LuraLura Powell Powell ((AITAIT, Advanced Imaging Technologies), Advanced Imaging Technologies)

John John ReyndersReynders (Eli (Eli LillyLilly & Co.)& Co.)Richard A. Roberts Richard A. Roberts ((PfizerPfizer))

Ray Ray SalemmeSalemme ((LinguagenLinguagen; formerly, ; formerly, 3DP: J&J3DP: J&J))

Mick Savage Mick Savage (Consultant; formerly (Consultant; formerly MSI: MSI: AccelrysAccelrys))

Thanks!Thanks!

Graduate Fellowship Supporters:Graduate Fellowship Supporters:Daylight Chemical Information SystemsDaylight Chemical Information SystemsMDL Information SystemsMDL Information Systems

Other chemical informatics software companies Other chemical informatics software companies for infor in--kind donationskind donationsAlfred P. Sloan Foundation Alfred P. Sloan Foundation (Laboratory Informatics)(Laboratory Informatics)

Max and Jane MarshMax and Jane MarshMany others who have contributed time, advice, Many others who have contributed time, advice, and teachingand teaching

BibliographyBibliographyCalandraCalandra, Bob. “Bioinformatics knowledge vital to , 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.htmlmlHam, Becky. Ham, Becky. ““Bioinformatics.Bioinformatics.”” ChemistryChemistry Winter 2004Winter 2004, , 99--10.10.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.htmlHarmon, G.; Garfield, E.; Paris, G. et al.Harmon, G.; Garfield, E.; Paris, G. et al. ““Bioinformatics Bioinformatics in information science educationin information science education..”” Proceedings of the Proceedings of the ASIST Annual Meeting ASIST Annual Meeting 20022002, , 3939, 490, 490--491.491.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), 8383--84, 86.84, 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), J4J4--J7. DOI: J7. DOI: http://dx.doi.org/10.1038/nj6903http://dx.doi.org/10.1038/nj6903--04a04aSchofield, Helen; Wiggins, Gary; Willett, Peter. "Recent Schofield, Helen; Wiggins, Gary; Willett, Peter. "Recent developments in developments in chemoinformaticschemoinformatics education." education." Drug Drug Discovery TodayDiscovery Today September 2001September 2001, , 6(18),6(18), 931931--934. 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, 61, 6--10.10.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), 11--2.2.http://www.chemistry.org/portal/resources/ACS/ACSCohttp://www.chemistry.org/portal/resources/ACS/ACSCo

ntent/education/cpt/nl_cpt_spring2004.pdfntent/education/cpt/nl_cpt_spring2004.pdf

Chemical Informatics TextbooksChemical Informatics TextbooksLeach, Andrew R.; Gillet, Valerie J. An Leach, Andrew R.; Gillet, Valerie J. An Introduction to Introduction to ChemoinformaticsChemoinformatics. . KluwerKluwer, 2003. , 2003. ISBN 1ISBN 1--40204020--13471347--77GasteigerGasteiger,,JohannJohann;Engel, Thomas. ;Engel, Thomas. ChemoinformaticsChemoinformatics: A Textbook. Wiley: A Textbook. Wiley--VCH, VCH, 2003. ISBN 32003. ISBN 3--527527--3068130681--11BajorathBajorath, , JJüürgenrgen, Ed. , Ed. ChemoinformaticsChemoinformatics: : 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 1Humana, 2004. ISBN 1--5882958829--261261--44