October 2007 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] new arabidopsis runs
by Tom Michoel 31 Oct '07

31 Oct '07

Hi, With the latest LeMoNe code and no other jobs running on tornado, 4 runs were finished in about 5 days. Now we need some basic analysis to see if anything cell-cycle related is showing up ... then we can play with some parameters to see how they affect results. For the experienced people, the output is here: /group/biocomp/projects/segal/tomic/LeMoNe/results/Arabidopsis/20071023 xml/ : use -Xmx7000m to read these figs/ : figures for all modules, separated for each of the runs figs2/ : figures ranked by edge weight (using "max") figs3/ : figures ranked by edge weight (using "sum") 20071023_edges_max_ranked.txt, 20071023_edges_sum_ranked.txt : networks ranked by edge weight (using both ways to compute edge weights) 20071023_edges_1000.cys : cytoscape file with best 1000 edges for both networks moduleSet_##.txt : gene clusters for each run. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] AtPID: Arabidopsis thaliana protein interactome da...[Nucleic Acids Res. 2007] - PubMed Result
by Yves Van de Peer 28 Oct '07

28 Oct '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] in Brussels
by Eric Bonnet 26 Oct '07

26 Oct '07

Hi there, Just to let you know that I'm in brussels today, for a begrid tutorial. have fun & a nice week-end! eric

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[Beg-sysbiol] working at home this morning
by Steven Maere 24 Oct '07

24 Oct '07

Hi gals and guys, I forgot all about it, but Brittje has a 'pedagogical study day' at school, which means she has to stay at home, so I'll be working from here till Marijke gets back around 11.00... S -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 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] LeMoNe update
by Tom Michoel 23 Oct '07

23 Oct '07

Hi, All the latest code is in the repository now. I don't foresee any major changes anymore, so this could be a good time to update. To use "Run", you will have to add values for new parameters in your properties file, see attached file for an example. "RunXml" contains some sample code to process xml files. The javadoc documentation is here: /group/biocomp/projects/segal/java/javadoc/index.html Have fun, Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/> # LeMoNe properties file # # Data directory dataDir=/group/biocomp/projects/segal/java/test_data/Challenge_5 # # Expression data, tab delimited file in format: # - line 1: description of conditions # - column 1: gene names # - column 2: gene description expressiondata=data.txt # Data type (AFFY or RATIO) dataType=AFFY # Candidate regulators file regulatordata=tfs.csv # # Perform initial clustering? (true/false) initClust=true # # If you said false to initial clustering, give initial number of clusters # and cluster file, in format: # - each line has a gene name and cluster number # - cluster numbers start with 0 or 1, comment lines (#) are discarded #numclust= #clusterdata= # # Statistical parameters used for the Bayesian score lambda0=0.1 mu0=8.5 alpha0=0.1 beta0=0.1 # # Use Gibbs sampling or heuristic search to optimize modules (=gene clustering)? (true/false) gibbsSampleGenes=true # # If you said true to Gibbs sampling genes, set Gibbs sampler properties: # - number of runs numRunsGenes=3 # - number of steps in each run numStepsGenes=100 # - number of initial steps before sampling starts burnInGenes=10 # - number of steps between samples sampleStepGenes=100 # # If you said false to Gibbs sampling genes, set heuristic search convergence cutoff # and whether or not you want an output file with all score values during search # (convergence is measured in Bayesian score per gene) #epsConvergence=0.001 #returnScore=false # # Use Gibbs sampling or heuristic search to optimize experiment partitioning within a module? (true/false) gibbsSampleExpts=true # If you said true to Gibbs sampling experiments, set Gibbs sampler properties: # - number of runs numRunsExpts=1 # - number of steps in each run numStepsExpts=1100 # - number of initial steps before sampling starts burnInExpts=100 # - number of steps between samples sampleStepExpts=100 # # Make one consensus regulation tree out of different experiment partitions? (true/false) makeConsensusTree=true # If you said true to makeConsensusTree, give level where trees should be cut before making consensus, # minimum number of experiments in one consensus experiment cluster, and the factor to determine significant # splits cutLevel=1 minSizeExpt=15 signiFact=1.0 # # Score cutoff for pruning regulation trees (measured in Bayesian score per gene) scoregain=0.0 # # Use merge score from Bayesian Hierarchical Clustering or simple score difference # when hierarchically clustering experiments or experiment clusters? (true/false) useBHCscore=true # # Assign regulators to tree nodes stochastically or deterministically (minimum entropy)? (true/false) assignRegStoch=true # if you said true to assigning regulators stochastically, set number of regulators per node # and probability parameter beta numReg=100 betaReg=20 # Assign regulators to all levels or only down to certain level; if you say false to assignAllLevels, set the # desired level depth in assignRegLevel assignAllLevels=false assignRegLevel=2 # if you said false to assigning regulators stochastically, do you want an acyclic network? (true/false) acyclic=false # # name of XML file (without extension) to store output, # if set to 'auto' an automatic name based on date and time of run is made. XMLfilename=auto # # # Enable/disable BiNGO GO tests on modules # Be sure to have a copy of the bingo_gui.properties file # in the current directory before setting this option to "true" BiNGO=false # # Enable/disable module drawing drawModules=false

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[Beg-sysbiol] paper
by Eric Bonnet 22 Oct '07

22 Oct '07

Another paper from vidal, integrating all kinds of omics data Network modeling links breast cancer susceptibility and centrosome dysfunction http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.2007.2.html

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[Beg-sysbiol] ENFIN A Network to enhance Integrative Systems Bio...[Ann N Y Acad Sci. 2007] - PubMed Result
by Yves Van de Peer 22 Oct '07

22 Oct '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] Computation Intelligent for Eukaryotic Cell-Cycle ...[Conf Proc IEEE Eng Med Biol Soc. 2006] - PubMed Result
by Yves Van de Peer 22 Oct '07

22 Oct '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] working @ home
by Steven Maere 17 Oct '07

17 Oct '07

I'm feeling a bit feverish and my throat is aching, so I'll work at home today (I don't want to infect certain pregnant women ;-) ) S -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 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] Theory and limitations of genetic network inferenc...[Ann N Y Acad Sci. 2007] - PubMed Result
by Yves Van de Peer 14 Oct '07

14 Oct '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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