[BiO BB] Introducing into Bioinformatics

Taylor, Deanne Deanne.Taylor at pfizer.com
Wed Feb 14 09:55:20 EST 2001

Besides the books that Gary listed, there really aren't any "Here's how to
become a cutting-edge bioinformaticist" books out there. Bioinformatics is
so new that most books that come out are all about the tools that exist, not
how to build new or better tools. As a programmer, I doubt you'll want to
sit back and use other people's tools. :) but those are just the books!
There is so much for a programmer to do in bioinformatics that books just
can't touch.

Ah, but one or two more books. :)  If you're of a mathematical bent, you may
want to at least check out of the library Eddy's book  "Biological Sequence
Analysis" by Durbin, Eddy, Krogh and Mitchison. There are several new
bioinformatics books out there that have just come out (search
"bioinformatics" on Amazon.com), though from what I've seen they're on the
level of Baxevanis, which is pretty much user-level stuff....how to use
other people's software.

Now, as a programmer, bioinformatics can become pretty much just about
handling data sets. If you want to do the science of bioinformatics, you
should follow what Gary said, definitely, and read up on the Mol. Bio of the
Cell. Also is the book GENES VII by Ben Lewin for genomic info. If you want
to work with genome or sequence information, you should know about stuff
like open reading frames, restriction sites, and how the data is generated
(PCR, etc).

In addition to sequence manipulation, there are several avenues a programmer
can explore. One is pure database handling, which reduces the bioinformatics
problem down to a data structure level. For instance, expression profiles
from chip data can be pretty  big databases at big companies. Oracle is used
a lot in many companies for this purpose. Additionally, data analysis and
statistics are valuable, though many chip manufacturers supply the analysis
programs so there isn't a need to do any more than understand what's going
on when one is doing this kind of analysis.

The bioinformatics field is really wide open as far as what one can do with
the data sets. Manipulating large data sets is going to become very
important in industry soon, including database work, because the real
information isn't in the "genome"...it's in how the cells express it, and to
do true expression profiling work takes thousands of experiments with many
many data points. 

Also coming up in importance in industry is pharmo-chemical profiling...mix
expression profiling with chemical profiles. Again, all database work but
statistics become important since there are no commercial/validated programs
for pharmochemical profiling so someone has to both set up the database
schema as well as work on the validation of data sets.

Summary:  iif you want to be on the cutting-edge of bioinformatics, have a
basic knowledge of statistics and validation, Perl and/or Python,
Oracle/SQL, molecular biology and genetics. You can be a bioinformaticist
without knowing much about mol bio and genetics, but you'll be more like a
data handler (which most bioinf programmers are these days).

Deanne Taylor

-----Original Message-----
From: Gary Van Domselaar [mailto:gvd at penguin.pharmacy.ualberta.ca]
Sent: Wednesday, February 14, 2001 9:30 AM
To: im99_foa at nada.kth.se
Cc: BIO Bulletin Board
Subject: Re: [BiO BB] Introducing into Bioinformatics


One of the best-selling books on bioinformatics is "Bioinformatics - A
Practical Guide to the Analysis of Genes and Proteins," Baxevanis and
Oulette (Wiley, 1998)".  I found it to be very accessible.  Another early,
but still valuable book is "Sequence Analysis Primer" by Gribskov (1991).
A less accessible, but still valuable book IMO, is "Bioinformatics, The
Machine Learning Approach" by Baldi and Brunak.  If you have no biology
background, you might want to pick up a good molecular biology text.
"Molecular Biology of the Cell" by James Watson (of Watson/Crick fame) is
very good.


--                                                                   --
                             Gary Van Domselaar
Ph.D. Candidate,                                    Associate Director,
Faculty of Pharmacy,                   Bioinformatics.org: The Open Lab
University of Alberta                           gary at bioinformatics.org
gary at penguin.pharmacy.ualberta.ca        http://bioinformatics.org/gary
--                                                                   --

On Wed, 14 Feb 2001, Marielle Fois wrote:

> Hello,
> Does anybody have an idea of a good way of getting into bioinformatics
> for someone on computer science with no biology background? I wonder
> if there is a book or article considered the standard in
> bioinformatics. Wouldn't this be a good information to have in this
> site?
> Thanks,
> Marielle
> _______________________________________________
> BIO_Bulletin_Board maillist  -  BIO_Bulletin_Board at bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board

BIO_Bulletin_Board maillist  -  BIO_Bulletin_Board at bioinformatics.org

More information about the BBB mailing list