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) http://www.iscb.org/univ.shtml

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 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 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/public at/primer2001/index.html http://www.ornl.gov/TechResources/Human_Genome/public at/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 Scientist September 2, 2002, 16(17). http://www.thescientist.com/yr2002/sep/prof1_020902.html 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 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 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.