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 s_equence file_ (nucleotides/protein)*/ in a wild type form, with start and stop codon/* / *- the organism of origin */ - the _contact emai_l 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* BASF Plant Science Company GmbH Legal Headquarter 67056 Ludwigshafen, Germany Registration Office: Amtsgericht Ludwigshafen Eintragungsnummer HRB 4516Lu Executive Management: Peter Eckes, Jürgen Schweden, Marc Ehrhardt -- 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/ --------------------------------------------------------- Come on out and change the world (around us)