Transcript Bioinformatics Instruction at US Research Universities (and elsewhere) Gary Wiggins School of Informatics Indiana University [email protected].

Bioinformatics Instruction at
US Research Universities
(and elsewhere)
Gary Wiggins
School of Informatics
Indiana University
[email protected]
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
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Successful bioinformatics systems are
built on:
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software development (algorithms and
database design)
visualization
user-interface development
Qualities of Bioinformaticians
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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
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Practical, problem-oriented focus in high demand
Much high-quality research now done in industry
Academia a safer path

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Not directly tied to the economy
Grants available for applied work
Drawbacks to academia:
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Publish-or-perish mentality
No horizontal career development path
Bioinformatics Job Prospects
(cont’d)
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US biotechnology industry concentrated
in nine metropolitan areas:
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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
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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)
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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

Over half of the programs began in the last three
years!
Survey: Bio1nf0rm 2003
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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
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Degree Programs
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59 US academic institutions are listed as of
December 13, 2003
http://www.bio-itworld.com/careers/biotrain/
Directories: University of North
Carolina
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Survey of Bioinformatics Programs (July
2003)
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Lists 49 universities
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http://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Brief_7-13-03.htm
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More details are available at:
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http://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Complete_7-13-03.xls
Directories: ISCB
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The International Society for
Computational Biology
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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
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University Bioinformatics Programs
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Only 12 US institutions
Last updated: July 23, 1998
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http://biotech.icmb.utexas.edu/pages/bioinform/biprograms_us.html
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Top Bioinformatics Graduate
Schools in the US
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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
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MS in Bioinformatics
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Two-year program
30 semester hours of coursework plus 6
semester hours of capstone project
PhD in Science Informatics
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Anticipated to start in fall 2005
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
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
/PRDFhomepage.htm
Flybase Drosophila Genome Database
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http://flybase.bio.indiana.edu/
UKeU MSc in Bioinformatics
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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
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UKeU: UK eUniversities Worldwide
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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
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Established in 1988 as a national resource for
molecular biology information
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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
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Three-day course for librarians with limited or
no previous experience searching molecular
sequence databases
Covers:
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nucleotide sequences
protein sequences
three-dimensional structures
complete genomes and maps
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http://www.ncbi.nlm.nih.gov/Class/MLACourse/index.html
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NCBI Advanced Workshop for
Bioinformatics Information Specialists
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Five-day course designed for those who
work in medical libraries
Cost:
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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
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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?”
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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
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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
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Guide to Selected Internet
Bioinformatics Resources by Christy
Hightower
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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
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Biocomputing in a Nutshell
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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)
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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
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E. Birney et al., "Databases and tools for
browsing genomes," Annual Review of
Genomics and Human Genetics, 3:293-310,
2002.
"The Molecular Biology Database Collection:
an online compilation of biological database
resources." (Published annually in the first issue of
the journal Nucleic Acids Research )
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http://nar.oupjournals.org/
Bioinformatics Books
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Many available:
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Amazon.com had 563 titles on 4/13/2004;
most popular:
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Bioinformatics: Genes, Proteins, and Computers
(Springer Verlag, 2003)
Indiana University Libraries held 135 titles
on 4/13/2004
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.html
Dahms, A.S. “Biotechnology education (editorial).” Biochemistry
and Molecular Biology Education 2001, 29(3), 121-122.
Ham, Becky. “Bioinformatics.” Chemistry Winter 2004, 9-10.
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.
Bibliography (cont’d)
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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.” bio1nf0rm August 11,
2003, 7(32), 1, 6-10.
Zauhar, Randy. “University bioinformatics programs on the rise.”
Nature Jobs Biotechnology March 2001, 19(3), 285-286.