Bioinformatics Instruction at US Research ... - Indiana University

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2 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

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Bioinformatics Instruction at
US Research Universities

(and elsewhere)

Gary Wiggins

School of Informatics

Indiana University

wiggins@indiana.edu

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


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.php


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.html

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 l
ibrarians 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.html


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/public
at/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.