- beg-sysbiol@psb.ugent.be - maillist.psb.ugent.be

[Beg-sysbiol] VIB work program 2006 systems biology subgroup
by Steven Maere 06 Oct '06

06 Oct '06

Hi Ann, Here's some text for the work program. Let me know if sth needs to be changed or shortened (probably too many references?). Steven -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group Ghent University / VIB Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3692 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] Re: Fwd: VIB- report 2006 and work program 2007
by Roeland Merks 04 Oct '06

04 Oct '06

Dear Systems Biology's, Have you started writing this report yet? If so, could you let me know what you have done so far, because I should probably fit my part on modeling into what you have already written... Thanks! Cheers, Roeland > Dear, > > as confirmed by the management, we can organize the report using the > mailing-list topics. > As such, each group/topic can produce the required text (see mail Ann). > > Current topics from the mailing-lists: > ? might be removed from the topic for this report focusing on the > future; I added some people that were currently missing (feel free to > modify) > > * Annotation > o liste, strom, strob?, erbon, yvsae, jawuy?, pirou, yvpee, > jefaw, frdie, mibel(IWT-pending), kenny? > * Evo-devo :: gene family evolution & duplicates > o cimar, tiblo, strob, ticas, stmae?, stbod?, klpoe?, yvpee, > pedro(IWT-pending) > * Transcriptional regulation > o thabe(IWT-pending?), klpoe, stbod, ticas?, , strob?, pirou, > yvpee, karen(IWT-pending) > * Systems biology & modeeling > o erbon, tomic, bemah, romer, stmae, yvsae, yvpee, anagha, bemah > > Guy Baele? > Dirk Gevers? > > good luck! > > >>> >>> >>> >>> Ann Bostyn wrote: >>>> Hello??? :-) >>>> >>>> There's not that much to do, so if you guys and girls give me a >>>> (little) >>>> hand, we can have this done in no time! Preferably by the end of the >>>> week.... :-) >>>> What we need is this: >>>> 1. list of research topics and staff members (no undergraduate >>>> students) >>>> working on >>>> these research topics; stating if they are fully or partly working >>>> on this >>>> topic; *people that have left during 2006, please indicate their >>>> departure >>>> date, people that will start after October 2006, please indicate >>>> their start >>>> date.* >>>> 2. general description and formulation of the scientific question(s) >>>> referring to scientific/ecomonic(?) relevance of the question(s) >>>> and the >>>> international state of affairs (reference to literature): please ask >>>> Christine for more info about this! >>>> 3. long term objectives (target 2011) in bullet points >>>> 4. short term objectives (target 2007) in bullet points >>>> 5. work program 2007 in bullet points (can be joined with (6) as in >>>> previous >>>> reports) >>>> >>>> I will put everything together. >>>> I have enclosed the work programme of 2004 as a reference. >>>> So I hope you can do this effort and give me a hand. >>>> Thanks a lot in advance! >>>> >>>> Ann >>>> >>>> -----Original Message----- >>>> From: Yves Van de Peer [mailto:yves.vandepeer@psb.ugent.be] Sent: >>>> donderdag 28 september 2006 22:16 >>>> To: Bioinformatics & Evolutionary Genomics >>>> Subject: [Fwd: VIB- report 2006 and work program 2007] >>>> >>>> >>>> >>>> Dear all, >>>> >>>> Since I'm terribly busy, I could use some help in this. If we >>>> divide the work, and we all do a little bit, this should not be too >>>> much of a burden. Is there someone who could coordinate this a bit >>>> (together with Ann?). >>>> >>>> Thanks in advance, >>>> >>>> Yves >>>> >>>> -------------------- >>>> >>>> >>>> Dear PI, >>>> VIB-HQ is asking us to deliver our *WORK PROGRAM 2007* >>>> >>>> The work program describes for each group the following elements: >>>> >>>> 1. name of the group leader >>>> 2. research topics >>>> 3. list of staff members (no undergraduate students) working on >>>> these research topics; stating if they are fully or partly >>>> working on this topic; *people that have left during 2006, >>>> please indicate their departure date, people that will start >>>> after October 2006, please indicate their start date.* >>>> 4. general description and formulation of the scientific >>>> question(s) referring to scientific/ecomonic(?) relevance of >>>> the question(s) and the international state of affairs >>>> (reference to literature) >>>> 5. long term objectives (target 2011) in bullet points >>>> 6. short term objectives (target 2007) in bullet points >>>> 7. work program 2007 in bullet points (can be joined with >>>> (6) as >>>> in previous reports) >>>> 8. bibliography >>>> >>>> We propose that small groups stick to _two pages_ and larger groups >>>> to _four pages_ (depending on the number of topics in the group) >>>> >>>> * *DO NOT USE STYLES OR FORMATTING* >>>> * *NO PAGE NUMBERS* >>>> * *NO FIGURES, TABLES,....* >>>> >>>> *Last year we did not have to make this report so the last report >>>> that was made was in October 2004. This report is put as an example >>>> on the P-drive under chtir in the folder "VIB" >>>> >>>> Deadline: October 9th >>>> >>>> *Many thanks in advance, >>>> Kind regards, >>>> Dirk >>>> Christine >>>> >>>> >>> >> >> -- Roeland Merks Department of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Ghent, Belgium http://www.psb.ugent.be Tel. +32-(0)9-33 13695 email: post(a)roelandmerks.nl http://www.roelandmerks.nl weblog: http://biolog.volkskrantblog.nl

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[Beg-sysbiol] Pôles d'Attraction Interuniversitaire
by Yves Van de Peer 03 Oct '06

03 Oct '06

http://www.inma.ucl.ac.be/IAPV/IAPDay.html

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[Beg-sysbiol] FYI
by Yvan Saeys 28 Sep '06

28 Sep '06

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[Beg-sysbiol] FYI: new koller paper
by Steven Maere 18 Sep '06

18 Sep '06

Alternative and apparently powerful application of module network learning formalism... S

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[Beg-sysbiol] Confidential
by Yvan Saeys 18 Sep '06

18 Sep '06

Hi all, I'm reviewing the attached paper on Genetic Networks. Although it's a bit vague and not detailed enough, maybe we can get some ideas from it, but please don't distribute and keep confidential. yvan -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://www.psb.ugent.be/bioinformatics/ http://www.psb.ugent.be/~yvsae/ ==================================================================

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[Beg-sysbiol] Confidential
by Yvan Saeys 18 Sep '06

18 Sep '06

Hi all, I'm reviewing the attached paper on Genetic Networks. Could be of interest for us, but please don't distribute and keep confidential. yvan -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://www.psb.ugent.be/bioinformatics/ http://www.psb.ugent.be/~yvsae/ ==================================================================

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[Beg-sysbiol] What about LeMoNe (Learning Module Networks) as a name for our package ?
by Steven Maere 15 Sep '06

15 Sep '06

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[Beg-sysbiol] solved hang-ups (?)
by Tom Michoel 30 Aug '06

30 Aug '06

The seemingly random hang-ups of the program were due to testCycle getting into an infinite loop. I added some extra cyclicity tests in assignRegulators() where I thought they were not necessary and it seems to solve the problem. Both ModuleNetworks in trunk and release have been corrected, so an svn update on your favorite version will do the trick. Tom

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[Beg-sysbiol] tiny update
by Steven Maere 25 Aug '06

25 Aug '06

Just to let you know that I removed the BiNGO folder from svn. From now on, this folder and the bingo_gui_properties file should be located in 'dataDir' (i.e. /test_data/ for our purposes, I've put all the stuff there). Cheers, Steven -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group Ghent University / VIB Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3692 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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