Bioinformatics Instruction at
US Research Universities
(and elsewhere)
Gary Wiggins
School of Informatics
Indiana University wiggins@indiana.edu

Abstract
Bioinformatics is a "hot" topic in US academic institutions since the completion of the
Human Genome Project and the availability of many other genomes for model organisms. Consequently, a large number of
US universities have established graduate programs in the field of bioinformatics. A review of the programs, their emphases, the problems faced in implementing a curriculum in bioinformatics, and the job prospects for graduates will be presented.

Bioinformatics Definition

Bioinformatics is an interdisciplinary approach requiring sophisticated computer science, mathematics, and statistical methods, with a deep understanding of the biological and chemical context, problems, and methodology behind the data.

Bioinformatics Definition
(cont’d)

It encompasses the storage, retrieval, and analysis of gene sequence, biological, pharmacological, and structural data; prediction of protein structure, function, and post-translational modification; prediction of protein-protein interactions; and the design of new computational tools to extract new correlations from large datasets.

Bioinformatics Tools

The systems developed in bioinformatics are built around data warehousing, data visualization, and the combination of clinical data with genetic data on very large scales.

Bioinformatics Training

Training in bioinformatics needs to go beyond acquiring the skills to use existing tools. Bioinformaticists need to have a very strong understanding of the methods they must use and understand clearly the strengths and weaknesses of the tools.

Bioinformatics Training
(cont’d)

They must be able to select the best solution to a given problem, quickly grasping the biological complexity of the problem and selecting from the available resources and techniques the best possible solution to that problem.

Bioinformatics Systems

Successful bioinformatics systems are built on:


 software development (algorithms and database design) visualization user-interface development

Qualities of Bioinformaticians



Ideally knowledge of computer science
AND biology
Organic chemists with a modeling mentality
Databases and programming skills (SQL and Oracle; C++, Perl, JAVA)

Bioinformatics Job Prospects


Industry more attractive than academia


Practical, problem-oriented focus in high demand
Much high-quality research now done in industry
Academia a safer path

Not directly tied to the economy


Grants available for applied work
Drawbacks to academia:


Publish-or-perish mentality
No horizontal career development path

Bioinformatics Job Prospects
(cont’d)


US biotechnology industry concentrated in nine metropolitan areas:


Boston, Los Angeles, New York,
Philadelphia, Raleigh-Durham, San Diego,
San Francisco, Seattle, and Washington,
DC/Baltimore
Many states are investing in biotechnology
Investment in biotechnology increasing

Bioinformatics Starting
Salaries & Opportunities




BS: $40,000-$50,000
PhD: over $100,000
Average salary: $65,000
Over 20,000 new jobs expected by
2005 according to the NSF

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!

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

Directories: Bio-IT World

Degree Programs


59 US academic institutions are listed as of
December 13, 2003 http://www.bio-itworld.com/careers/biotrain/

Directories: University of North
Carolina

Survey of Bioinformatics Programs (July
2003)



Lists 49 universities http://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Brief_7-13-03.htm
More details are available at: http://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Complete_7-13-03.xls


Directories: ISCB

The International Society for
Computational Biology




Listing of Degree/Certificate Programs
Worldwide: 49 programs
28 of the 49 programs are in the US as of
4/13/2004 http://www.iscb.org/univ_programs/program_board.php
http://www.iscb.org/univ.shtml
(earlier ISCB listing)

Directories: University of
Texas

University Bioinformatics Programs


Only 12 US institutions
Last updated: July 23, 1998 http://biotech.icmb.utexas.edu/pages/bioinform/biprograms_us.html


Top Bioinformatics Graduate
Schools in the US







Stanford University (8)
University of California, Santa Cruz (5)
Boston University (4)
University of California, San Diego (4)
Harvard (4)
University of Washington (3)
28 schools got at least one vote from the 10 respondents.

Bioinformatics Degrees at
Indiana University


MS in Bioinformatics


Two-year program
30 semester hours of coursework plus 6 semester hours of capstone project
PhD in Science Informatics

Anticipated to start in fall 2005

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

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

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/

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

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=

NCBI: National Center for
Biotechnology Information


Established in 1988 as a national resource for molecular biology information

Creates public databases



Conducts research in computational biology
Develops software tools for analyzing genome data
Disseminates biomedical information http://www.ncbi.nlm.nih.gov/

NCBI Introduction to
Molecular Biology Resources


Three-day course for librarians with limited or no previous experience searching molecular sequence databases
Covers:
 nucleotide sequences


 protein sequences three-dimensional structures complete genomes and maps
 http://www.ncbi.nlm.nih.gov/Class/MLACourse/index.html

NCBI Advanced Workshop for
Bioinformatics Information Specialists


Five-day course designed for those who work in medical libraries
Cost:



No registration fee for the course
Participants must cover their own travel, hotel, and meals.
http://www.ncbi.nlm.nih.gov/Class/NAWBIS/

NLM Senior Fellowship for
Informationists


Purpose: to improve biomedical research and education, and public health administration
How? By including in-context information specialists (informationists) into work and decision settings
 http://grants.nih.gov/grants/guide/pa-files/PAR-04-014.html

What are “informationists?”

Information specialists who have received graduate training and practical experience that provides them with disciplinary background both in medical or biological sciences and in information sciences/informatics

National BioInformatics Institute




Beware of this site!
Offers a certification program for bioinformatics and cheminformatics
Most of their materials are “borrowed” without permission from other Web sites http://www.bioinfoinstitute.com/default.htm

Bioinformatics Web Resources I

Guide to Selected Internet
Bioinformatics Resources by Christy
Hightower

A very selective guide, focusing on human sources


Issues in Science and Technology
Librarianship (Winter 2002) http://www.istl.org/istl/02-winter/internet.html

Bioinformatics Web Resources II


Biocomputing in a Nutshell
 http://www.techfak.unibielefeld.de/bcd/ForAll/Basics/welcome.html
Genomics and Its Impact on Science and Society:
The Human Genome Project and Beyond (2003)

Includes Genomics 101, the update to the 1992 Primer on
Molecular Genetics
 http://www.ornl.gov/TechResources/Human_Genome/publica t/primer2001/index.html

Bioinformatics Databases


E. Birney et al., "Databases and tools for browsing genomes,"
2002.
Annual Review of
Genomics and Human Genetics , 3:293-310,
"The Molecular Biology Database Collection: an online compilation of biological database resources." (Published annually in the first issue of the journal Nucleic Acids Research )
 http://nar.oupjournals.org/

Bioinformatics Books

Many available:


Amazon.com had 563 titles on 4/13/2004; most popular:

Bioinformatics: Genes, Proteins, and Computers
(Springer Verlag, 2003)
Indiana University Libraries held 135 titles on 4/13/2004

Bibliography




Calandra, Bob. “Bioinformatics knowledge vital to careers.” The
Scientist September 2, 2002, 16(17). http://www.thescientist.com/yr2002/sep/prof1_020902.html
Dahms, A.S. “Biotechnology education (editorial).” Biochemistry and Molecular Biology Education 2001, 29(3), 121-122.
Ham, Becky. “Bioinformatics.”
Chemistry%5Cindex.html
Chemistry Winter 2004, 9-10. http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=
Harmon, G.; Garfield, E.; Paris, G. et al. “Bioinformatics in information science education.” Proceedings of the ASIST
Annual Meeting 2002, 39 , 490-491.

Bibliography (cont’d)




Henry, Celia M. “Careers in bioinformatics.” Chemical &
Engineering News April 8, 2002, 80(14), 83-84, 86.
Marasco, Corinne A. “Career paths abound in biotech.” Chemical
& Engineering News December 8, 2003, 81 , 49, 52, 56.
Toner, Bernadette. “Number of bioinformatics grads grows, but rise in degree programs slows in 2003.”
2003, 7(32), 1, 6-10.
bio1nf0rm August 11,
Zauhar, Randy. “University bioinformatics programs on the rise.”
Nature Jobs Biotechnology March 2001, 19(3), 285-286.