Bioinformatics Instruction at US Research Universities (and elsewhere)

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

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

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

9. 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)

10. 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

11. 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

12. 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

13. 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!

14. 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

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

16. 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

17. 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)

18. 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

19. 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.

20. 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

21. 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

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

23. 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/

24. 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

25. 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=

26. 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/

27. 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

28. 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/

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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/

35. 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

36. Bibliography • Calandra, Bob. “Bioinformatics knowledge vital to careers.” The ScientistSeptember 2, 2002, 16(17). http://www.thescientist.com/yr2002/sep/prof1_020902.html • Dahms, A.S. “Biotechnology education (editorial).”Biochemistry and Molecular Biology Education2001, 29(3), 121-122. • Ham, Becky. “Bioinformatics.” ChemistryWinter 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.

37. Bibliography (cont’d) • Henry, Celia M. “Careers in bioinformatics.” Chemical & Engineering NewsApril 8, 2002, 80(14), 83-84, 86. • Marasco, Corinne A. “Career paths abound in biotech.” Chemical & Engineering NewsDecember 8, 2003, 81, 49, 52, 56. • Toner, Bernadette. “Number of bioinformatics grads grows, but rise in degree programs slows in 2003.” bio1nf0rmAugust 11, 2003, 7(32), 1, 6-10. • Zauhar, Randy. “University bioinformatics programs on the rise.” Nature Jobs BiotechnologyMarch 2001, 19(3), 285-286.