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
 Bioinformatics Programs
 Future

Comments on Chemical
Informatics as a Discipline
Jürgen Bajorath on
Chemoinformatics, etc.
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Chem-, chemi-, or chemo-informatics
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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
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Chemical Informatics: the application of
information technology to chemistry (not
with a specific focus on drug discovery)
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
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Discovery informatics—acknowledges that
gaining knowledge from chemical data
alone is insufficient for success in drug
discovery
Bajorath’s Conclusions
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Boundaries between bioinformatics and
chemoinformatics are fluid
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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.
Other Programs and Courses
Another Program in the US
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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
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Selected Courses in
Cheminformatics
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Introduction to Chemoinformatics Course at the
University of Michigan
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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/chemoinf
ormatics.htm
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Analytical Informatics at Purdue (Randy Julian)
http://miner.chem.purdue.edu/
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/marke
tingpackets/biochembrochure.pdf
 Chemoinformatics National BioInformatics
Institute
http://www.bioinfoinstitute.com/chemoinfo.htm
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Indiana University Programs in
Chemical Informatics
Specialized Chemistry Degree Options
at Indiana University
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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
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

Unique Program at IUPUI

Laboratory Informatics track at IUPUI
Instrumentation and data interfacing
 Laboratory notebooks
 Laboratory Information Management Systems
(LIMS)
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Why IU for Chemical Informatics?
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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
Core and Affilated Faculty at IUB
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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)
Core and Affilated Faculty at IUPUI
SAM A.F. MILOSEVICH
 MAHESH MERCHANT
 JOHN MCKELVEY (adjunct)
 DON BOYD (affiliated)
 KELSEY FORSYTHE (affiliated)
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Outreach Activities
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Research relationships with
IU School of Medicine
 IUB/IUPUI bioinformatics and proteomics
research programs
 Commercial firms through internships
(LeadScope, Rosetta Inpharmatics, Lilly)
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IU Undergraduate Courses
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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
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IU Graduate Courses
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Two three-credit graduate courses
C571 Chemical Information Technology
 C572 Molecular Modeling & Computational
Chemistry
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New courses under development
Programming for Chemical Informatics
 Information Retrieval from Chemistry and Life
Sciences Databases
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Tools Used or Planned for Use
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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]
Sharing Instruction
Problems
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
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Problem: Students with Little or No
Background in Science or CS
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Often MS students have good computer science
background, but little or no science training or vice versa
Solution: Remedial courses
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Chemical Foundation for Bioinformatics
http://www.poly.edu/catalog03-05/catalog03-05-21-bioinformatics.pdf
 Polytechnic University (Brooklyn)
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Introduction to Genomics
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A-level graduate courses in Computer Science
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Indiana University
Indiana University
Dilemma: Should remedial courses count toward the MS
degree?
Problem: Little exposure to
chemical informatics as undergrads
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Can a student really master chemical
informatics in a 1- or 2-year MS program?
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 Communications 2002, (23), 2745-2747. DOI:
10.1039/b207793k
http://xlink.rsc.org/?DOI=b207793k
Bioinformatics
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
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Bioinformatics Faculty at IUB
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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)
Bioinformatics Faculty at IUPUI
A. KEITH DUNKER
 ARIEL FERNANDEZ
 JEFFREY HUANG
 SNEHASIS MUKHOPADHYAY
 NARAYAN PERUMAL (visiting)
 MALIKA MAHOUI (visiting)
 ZINA BEN-MILED (adjunct)
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Directories: bio1nf0rm
(US only)
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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
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Over half of the programs began in the last three
years!
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
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UKeU: UK eUniversities Worldwide
Established in 2001
 For students anywhere in the world
 Has a global service support
infrastructure - available 24x7
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http://www.ukeu.com/index.php?site=
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
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http://www.ukeu.com/courses/bioinformatics/courses_bioinformatics.php?site=students
Indiana Initiatives
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Indiana Genomics Initiative
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Inproteo (Indiana Proteomics Consortium)
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http://www.ingen.iu.edu/
http://www.inproteomics.com/index.html
Bio Crossroads (Central Indiana Life
Science Network)
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http://www.biocrossroads.com/default.htm
Indiana University’s
Bioinformatics Initiatives: Indy
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Center for Computational Biology and
Bioinformatics at Indianapolis
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http://www.compbio.iupui.edu/
Indiana University’s
Bioinformatics Initiatives: IUB
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Center for Genomics and Bioinformatics
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Biocomplexity Institute
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http://biocomplexity.indiana.edu/
Proteomics Research and Development Facility
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http://cgb.indiana.edu/
http://www.chem.indiana.edu/facilities/proteomics/PR
DFhomepage.htm
Flybase Drosophila Genome Database
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http://flybase.bio.indiana.edu/
Future
Future
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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
School of Informatics
Science Informatics Advisory Board
(as of 8/19/2004)
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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)
Thanks to Graduate Fellowship
Sponsors:
Daylight Chemical Information Systems
MDL Information Systems
Bibliography
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Calandra, Bob. “Bioinformatics knowledge vital to
careers.” The Scientist September 2, 2002, 16(17).
http://www.thescientist.com/yr2002/sep/prof1_020902.ht
ml
Ham, Becky. “Bioinformatics.” Chemistry Winter 2004, 910.
http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?D
OC=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 News April 8, 2002, 80(14), 83-84, 86.
Bibliography (cont’d)
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Russo, Eugene. “Chemistry plans a structural overhaul.”
Nature September 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 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.
Wiggins, Gary. “Teaching chemical literature, databases,
and chemical informatics.” CPT; Committee on
Professional Training [newsletter] Spring 2004, 4(1), 12.
http://www.chemistry.org/portal/resources/ACS/ACSCon
tent/education/cpt/nl_cpt_spring2004.pdf
Chemical Informatics Textbooks
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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