Bioinformatics Instruction at US Research

Universities (and elsewhere)

Gary WigginsSchool of Informatics

Indiana Universitywiggins@indiana.edu

AbstractBioinformatics 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.p

hp 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.ht

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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.ht

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Bioinformatics Web Resources II

Biocomputing in a Nutshell http://www.techfak.uni-bielefeld.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/

publicat/primer2001/index.html

Bioinformatics Databases 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 ) 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 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) 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.