BioInformatics Curriculum

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Wed Apr 13 13:30:38 EST 2005

"Meshktenye" wrote:

> We want to assure our students that the training they
> receive will guarantee them a career in the field.

Unfortunately, with todays job market that is wishful thinking.

> What tools, resources, databases, software, manuals, specific training,
> education, knowledge, lab experience, lab equipment, etc. would be most
> helpful for an entry-level BioInformatics researcher to know? What
> tools would be most useful for Stem Cell Research?

In my experience most books and resources currently available fall into
2 categories:

a) Aimed at students with a background in maths/informatics. The
explanations for the various algorithms given is often way over the head
of a humble biologist. Remember that mathematical formulas allow a very
brief and precise statement of things, but require routine in
interpretation, which biologist often don't have. 

b) Aimed at students in biology. Algorithms are often not explained at
all, explanations are cookbook-like: For this problem use that program
and such-and-such database, and don't worry how it all works. 

Neither approach is IMHO satisfactory, the former is elitist and lazy,
the latter makes the student unable to judge the validity of the

If you need to train programming, I would advise the use of a clean
language like Logo or Modula-3 to introduce concepts and good
programming techniques. Only later should students be introduced to
languages that allow, if improperly used, bad programming style
(C-derivates). The Modula-3 homepage contains an interesting comparison
of Modula-3, Turbo-Pascal and C++ as training languages.

A brief introduction into LaTeX as publishing tool can save students a
lot of grief when they have to write their thesis. Literate programing
should also be covered, using language-independent tools like noweb. 

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