[BiO BB] Linear Bioinformatics workflow?

William Hsiao william.hsiao at gmail.com
Mon Oct 3 16:28:22 EDT 2005

Hi Amir,
   What about Pegasys
or Taverna (http://taverna.sourceforge.net/) as possible systems? 
These are graphical based system as well but they would be able to do
what you described below.



On 10/3/05, Amir Karger <akarger at cgr.harvard.edu> wrote:
> Several people mentioned 2-D graphical workflow tool in a "Bioinformatics
> workflow?" thread on bioclusters. (I'm redirecting my non-cluster-y question
> here.) While still a newbie, I'm getting the impression that many
> bioinformatics workflows are mostly linear, with obvious important
> exceptions like conditions and loops. For example, I had a client last week
> who wanted to script:
> 1 blast [sequence=..., program=...] > blast.out
> 2 get hits from blast.out > blast.hits
> 3 find hits with 50-70% sequence identity from blast.hits > blast.good_hits
> 3 download/fastacmd sequences for IDs in blast.good_hits > hits.fasta
> 4 clustalw hits.fasta > publishable_result (OK, not really)
> Our current model is to help people to write shell scripts, but that doesn't
> work for all users. It seems like a two-dimensional workflow tool would be
> overkill for the above. All I need is a tool that combines
> Pise/iNquiry-style "select a bioinformatics tool, input parameters" with the
> ability to save a set of commands.
> Of course, it would be much less powerful and flexible than the 2-D workflow
> tools. But "protocols" (http://biopipe.org/protocols/) might be an easier
> sell to computer-phobes than directed acyclic graphs.
> Is there anything out there that does this? I'd much rather steal than
> build.
> - Amir Karger
> Computational Biology Group
> Bauer Center for Genomics Research
> Harvard University
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William Hsiao
PhD Student, Brinkman Laboratory
Department of Molecular Biology and Biochemistry
Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada V5A 1S6
Phone: 604-291-4206 Fax: 604-291-5583

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