August 2006 - beg-sysbiol@psb.ugent.be

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

25 Aug '06

Dear all, After a few modifications to BiNGO.java and Module.java, removing all annoying GUI stuff, our program can now run in headless mode on the cluster nodes... I added RunHeadless.java in the repository (Release1 branch). However, I couldn't commit the other modified .java files (so it won't work yet), I got svn 'out of date' errors while the files were minutes old. Eric, any ideas ? Also, Tom, should I commit the modified TreeNode.java (for handling the NaN's) and ModuleNetwork.java (there was still this bit of code for handling the CS module overlap in there) to Release1 or not, what do you think ? And are there any other changes to the trunk code that should be added to Release1 (to avoid having versions that diverge too much) ? 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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[Beg-sysbiol] new journal
by Eric Bonnet 22 Aug '06

22 Aug '06

BMC Systems Biology http://www.biomedcentral.com/bmcsystbiol/

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[Beg-sysbiol] Entrez PubMed
by Yves Van de Peer 20 Aug '06

20 Aug '06

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

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[Beg-sysbiol] bingo plugged into software
by Steven Maere 11 Aug '06

11 Aug '06

Dear all, You can now use BiNGO to analyze the modules you find with our software (that is, if you use REAL data...), simply activate line 158 (BiNGO b = new BiNGO(M) ;) in Run.java. When compiling with this line activated, please be sure to include java/lib/cytoscape/cytoscape.jar, java/lib/cytoscape/BiNGO.jar and the java/lib/cytoscape/lib/ folder in your compiler path. To change BiNGO parameter settings, modify the relevant fields in BiNGO.java and bingo_gui_properties (or come to me, that's probably easier). It is now set for S. cerevisiae and GO_Biological_Process annotations, and it appears to work fine. Cheers, Steven

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[Beg-sysbiol] time frame for paper
by Tom Michoel 10 Aug '06

10 Aug '06

Hi, What do you think about finishing all computations 2 weeks from now (aug. 25)? Then we'll have about 2.5 weeks to actually write the paper, finish the release version of the code, and (for me) prepare a talk for the department meeting. As for the paper, I have written some short sections on module networks, learning regression trees, and assigning regulators, see attach. The LaTeX source uses the BMC style file and I put it under svn version control, so we can easily keep track of who changes what (checkout from file:///nas/biocomp/projects/segal/modnetBMC/). We can probably keep a Word version as well (converters exist), but I honestly cannot (nor want to for that matter :-) work with it. Tom

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[Beg-sysbiol] JCell—a Java-based framework for inferring regulatory networks,from time series data
by Roeland Merks 09 Aug '06

09 Aug '06

-- 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 13825 email: post(a)roelandmerks.nl http://www.roelandmerks.nl weblog: http://biolog.volkskrantblog.nl

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[Beg-sysbiol] [Fwd: ***UNCHECKED*** Re: [Fwd: [Fwd: hi there]]]
by Eric Bonnet 09 Aug '06

09 Aug '06

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[Beg-sysbiol] software update
by Tom Michoel 07 Aug '06

07 Aug '06

2 bug fixes in ModuleNetwork, required small changes in Module and TreeNode, see comments in svn log. this one is final ... at least until the next update :-) tom

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