Diverse Bioinformatics-Education Offerings Develop

Develop PHOTO CREDIT: Graham G. Ramsay DO IT YOURSELF: Harvard Medical School's George Church (back) thinks the best way to learn cutting-edge bioinformatics techniques is through constant self-education. Church and research assistants (from right) Jason Hughes, Preston Estep, and Fritz Roth (now with Millennium) stand near an RNA chip scanner, which helps determine changes in gene expression due to a given stimulus. Date: December 7, 1998 Asking five people to define bioinformatic

By | December 7, 1998

Develop

PHOTO CREDIT: Graham G. Ramsay


DO IT YOURSELF: Harvard Medical School's George Church (back) thinks the best way to learn cutting-edge bioinformatics techniques is through constant self-education. Church and research assistants (from right) Jason Hughes, Preston Estep, and Fritz Roth (now with Millennium) stand near an RNA chip scanner, which helps determine changes in gene expression due to a given stimulus.

Date: December 7, 1998

Asking five people to define bioinformatics yields seven different answers, jokes Scott D. Kahn, senior director of life sciences marketing at Molecular Simulations Inc., a San Diego bioinformatics software firm. Asking five people how to gain bioinformatics skills leads to a similar conundrum. Until recently, self-teaching remained the only recourse. Now, short courses, university coursework, Web-based learning, and commercial software tutorials have emerged. Each option comes with its own set of pluses and minuses:

Self-teaching For people who actually develop software, such as George Church, professor of genetics at Harvard University, who has been dabbling in bioinformatics since the ninth grade, this remains the only real recourse for staying on the forefront of the field. "It's a combination of reading the literature--both the computational and the biological literature--and reproducing the results--then extending them."

The upside? A sense of leading, rather than following. "The really cutting-edge stuff is not often recognized in the courses," Church states. The downside? Hard, time-consuming work. "You're going to have to dig."

Web-based tutorials Learning bioinformatics software via the Internet sounds like the most convenient means of education. "A manager in the pharmaceutical industry really can't afford to take six weeks off and go on a course," notes W. Graham Richards, professor of physical and theoretical chemistry at Oxford University. Unfortunately, few formal Web-based courses exist, although many universities are considering developing them.

Also, many of the free, public-domain tools that also contain tutorials are not centrally located or well maintained. "All these things are scattered all over the Internet," Boguski notes. "There are always the updating and dead-link problems."

John Salerno, who is helping set up undergraduate, graduate, and continuing education courses in bioinformatics at Rensselaer Polytechnic Institute in Troy, N.Y., thinks learning how to use bioinformatics tools over the Web best suits people who already have strong computer science, statistics, or math backgrounds. "I don't think that those Net-based courses are as useful for ... typical molecular biologists who want to go out and learn how to use bioinformatics tools, because it's just not that easy to break into them."

Short courses This option may be best for scientists wanting to learn a lot about one particular tool in a compressed time period. "If I were a molecular biologist and I had no computer science and I wanted to learn this, I would probably do a short course someplace," Salerno notes. However, short courses, at least now, are not exactly ubiquitous. And the strong ones that do exist are often oversubscribed, maintains Mark S. Boguski, senior investigator at the computational biology branch of the National Center for Biotechnology Information, adding that one at Johns Hopkins University has a waiting list.

Graduate and undergraduate courses These courses, which are fairly new or in development at several universities, tend to focus on how the underlying algorithms that drive, say, comparative genomics software, work. They may be especially useful for researchers interested in altering lab-based software or developing their own tools. "Then it isn't just a black box to you," explains Salerno. However, these offerings may place less emphasis on specific software.

Curriculum may also vary greatly from institution to institution. "Computational biology is still lacking a consensus on what a formal training program should be," Boguski notes, although he adds that people are coming up with suggestions (R.B. Altman, Bioinformatics, 14[7], 549-50, 1998). And for now, at least, universities seeking faculty expertise face the same issue as many biotech companies looking to beef up their bioinformatics teams--they often have only one or two experts in-house. That's not enough for a strong program, Boguski notes. "You need a critical mass of faculty--one [person] is not enough."

Commercial software, training included Although many early tools in bioinformatics--especially those dealing with raw genomic data--were lab built and often had no user-friendly interface, many new commercial tools are easier to use. Also, several firms offer on-site training. Kahn, whose company sells molecular modeling software, notes that this approach may be best for pharmaceutical companies. "There's more of an emphasis to use commercial software in the commercial area because added value does not come through rewriting tools that are already out there." Kahn adds that, with training, commercial software can be altered. "The experts can continue to muck around with the algorithms. Nonexperts, or the individual scientist, have access to tools that are well validated."

Lee Amon, of MDL Information Systems, San Leandro, Calif., thinks his company's policy of offering on-site training for its chemoinformatics packages serves as a strong selling point, because it saves time. "You should be able to get started faster." Many bioinformatics software companies include training, but tend to limit topics to their own products, though in reality computational biologists are likely to use a variety of tools, Boguski notes.

Boguski suspects that each means of training will find its specific audience--especially since the demand to learn seems so high. "I don't think anyone has the ideal formula for how to solve this problem. There will continue to be many kinds of ad hoc solutions to this: short courses, distance learning, a small degree of graduate training," he predicts. "I think these different flavors of solutions will continue to flourish, at least for the next several years."

Cold Spring Harbor Laboratory Meetings and Courses nucleus.cshl.org/meetings/99courses.htm

The Jackson Laboratory Training and Education www.jax.org/training/documents/

 

Bioinformatics Courses Worldwide bioinformatics.weizmann.ac.il/mb/tut/bioinfo_courses.html

European Molecular Biology Laboratory: Courses, Conferences and Workshops www.embl-heidelberg.de:432/CoursesConferences.htm

The International Society for Computational Biology Training programs in bioinformatics and computational biology www.icsb.org/training.html

 

European Bioinformatics Institute www.ebi.ac.uk/ebi_home.html

ExPASy Molecular Biology Server expasy.hcuge.ch/

GeneCards bioinformatics.weizmann.ac.il/cards

National Center for Biotechnology Information www.ncbi.nlm.nih.gov/

Pedro's BioMolecular Research Tools www.public.iastate.edu/~pedro/research_tools.htm

 

DNA Star Inc. www.dnastar.com/

Genetics Computer Group www.gcg.com/

MDL Information Systems Inc. www.mdli.com/

Molecular Simulations Inc. msi.com

Oxford Molecular Ltd. www.oxmol.com

Pangea Simulations Inc. panbio.com

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