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

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bioinformatics instruction at us research universities and elsewhere

Bioinformatics Instruction at US Research Universities (and elsewhere)

Gary Wiggins

School of Informatics

Indiana University

wiggins@indiana.edu

abstract
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 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
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
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
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
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
Bioinformatics Systems
  • Successful bioinformatics systems are built on:
    • software development (algorithms and database design)
    • visualization
    • user-interface development
qualities of bioinformaticians
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
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
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
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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.
bibliography cont d
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.