Dear,

who from sysbiol can join us in the week of April 19th to help? Preferably someone who has access to the Lemone/Enigma plant modules.

thanks,

Stefanie
Dirk
Klaas

Bioinformatics challenge:
Background info:
We all face the situation, that we have a gene sequence in our hand and don´t know the function. Usually we have limited time (max a few hours) to find data and to decide on whether the gene is of interest for us or not. We also have a limited understanding how good or bad we are in comparison to others, since a pure quantitative comparison of softwares and hardwares would only lead to limited results.
In order to compare our capabilities in a more qualitative way we agreed to do a joint test case by cross comparing our capabilities to find functions for a give gene (sequence).

The principle is a follows:
Each of the 4 entities (Dirk, Lothar, Xing Wang, Jürgen) will provide one gene sequence (out of yield area, where the respective entity is a specialist) to all other entities with request  to come up with suggestions about the function(s)  - time to deliver : one day (24hours). The entities are challenged to find out everything they can about that particular gene and a potential gene product. The respective gene providing entity  will compare the findings – what findings were similar, different, new, and why and will report to the others.
The results corresponding to the provided gene belong to the entity that provided the gene sequence.

Detailed workflow:
Each entity provides
        - a sequence file (nucleotides/protein) in a wild type form, with start and stop codon
        - the organism of origin
        - the contact email to Jürgen Logemann prior to the start time.
At 9:00 hrs german time Jürgen Logemann will distribute the 4 sequence files to all contact emails with a cc to the SAM members.
Each entity will work on the 3 sequences with approx. 2 FTEs.
24 hrs later, at 9:00 hrs german time the feedback of each entity has to be in the e-mail of Jürgen Logemann.
The feedback should be in a digestable form, so that a person, being not an expert understands the message (sequence, function, structure etc.)
Jürgen Logemann will distribute the feedback to all entities, the respective gene providing entity will check and compare/rank the content related to its gene
At the next SAM meeting all entities discuss the results by phone.

Open points:
- Metalife might join as a 5th entity (Jürgen L to check)
- We will need a short contract being signed before starting day, describing who owns what (Jürgen L and all)
        options: everybody owns his own results - everybody owns all results on his sequences
- What happens to the ownership of results, if one entity provides a gene sequence, where the other entity is also working on ? (all)
- The final day  for the challenge and for the results discussion needs to be agreed - week of April 19th ? (all)
- What about negative controls? What about also adding three random nucleotide sequences ( containing ORF´s obviously) (all)
- Do we need to define what description / annotation level we want to reach (all)



 
Juergen Logemann
Vice President Technology Management

Phone: +49 621 60-27204, Mobile: +49 172 7470513, Fax: +49 621 60-28685, E-Mail: juergen.logemann@basf.com
Postal Address: BASF Plant Science Company GmbH, BPS_TECM - LI439, 67117 Limburgerhof, Germany

BASF - The Chemical Company

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Klaas Vandepoele, PhD
Tel. 32 (0)9 33 13822
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, Belgium
E-mail: Klaas.Vandepoele@psb.vib-ugent.be
Website: http://bioinformatics.psb.ugent.be/
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