[BiO BB] BioInformatics Workbench project

J.W. Bizzaro jeff at bioinformatics.org
Fri Jun 23 19:10:22 EDT 2006

I agree with Oscar.  Bioinformatics is a small field but incredibly broad in 
scope.  Plus, "workbench" could mean a lot of things and is largely dependent 
on the user interface (are you thinking about a desktop or Web application?).

You should also consider the fact that there are a couple dozen applications 
out there that could be (and are) described as "bioinformatics workbenches", 
some being under well-funded development for years.  Here's a sample:

Taverna <http://taverna.sourceforge.net/>
Swami <http://www.ngbw.org/>
OpenFlow <http://www.openflow.it/EN/index_html>
GalaxiaWorkflow <http://tikiwiki.org/tiki-index.php?page=GalaxiaWorkflow>
Wildfire <http://wildfire.bii.a-star.edu.sg/wildfire/>
BIRCH <http://home.cc.umanitoba.ca/~psgendb/>
EMBOSS <http://emboss.org/>
wEMBOSS Portal <http://www.wemboss.org/>
WSBAW <http://www.alphaworks.ibm.com/tech/wsbaw>
SciCraft <http://www.scicraft.org/>
Scitegic <http://scitegic.com/products_services/pipeline_pilot.htm>
Pegasys <http://bioinformatics.ubc.ca/pegasys/>
ANGIS <http://www.angis.org.au/>
W2H <http://www.w2h.dkfz-heidelberg.de/>
Pise <http://www-alt.pasteur.fr/~letondal/Pise/>
SRS <http://www.biowisdom.com/solutions_srs.htm>

I suggest that your first objective would be to identify every "bioinformatics 
workbench" out there.  Your second objective should be to find out what none of 
them do (or do well).  And then propose a project to address that problem.


Oscar Moya wrote:
> Your project looks quite interesting but it sounds too broad to me. Could
> you give some examples of the kind of tools you would like to include in
> your package? Which are the problems you want to solve with your program?

J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600

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