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

[Beg-sysbiol] 2 interesting papers in MSB
by Tom Michoel 28 Nov '06

28 Nov '06

<http://www.nature.com/msb/journal/v2/n1/full/msb4100103.html> <http://www.nature.com/msb/journal/v2/n1/full/msb4100106.html> -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] sysbiol future
by Tom Michoel 22 Nov '06

22 Nov '06

We'll have a mini brainstorm on the future of the sysbiol group tomorrow at 2 p.m., mainly to discuss possible new research projects for the people that will be hired soon. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] news for computer geeks: java is now free
by Eric Bonnet 14 Nov '06

14 Nov '06

http://arstechnica.com/news.ars/post/20061113-8205.html

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[Beg-sysbiol] Appearently more and more of my colleagues in machine learning start tackling sysbiol :-)
by Yvan Saeys 10 Nov '06

10 Nov '06

http://www.cs.helsinki.fi/group/bioinfo/events/pmsb06/final/geurts_et_al.pdf -- ================================================================== 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://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ==================================================================

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[Beg-sysbiol] MCL clustering in Java
by Yvan Saeys 10 Nov '06

10 Nov '06

Hi all, As I was planning to test some different clustering algorithms anyway in the future of the segal project, I copied the Java code of MCL into .../java/MCL I should also say that with Thomas and our thesis student Andreas, we are implementing a JAVA clustering library, containing different types of clustering algorithms, which will be ready to use for different problems in bioinformatics and machine learning. This will make it easier in the future to try different clustering algorithms, e.g. prior to the network inference step. In the framework of my BOF-project I am now doing a literature study on different theoretical aspects of clustering, hoping to result in an updated taxonomy of different clustering algorithms, their internal relations, respective (dis)advantages and characteristics of the data/clusters they assume. In particular, my attention focuses on the aspects of data sets for clustering as they arise in bioinformatics, i.e. large dimensionality, noise, outliers, and other funny features that hampers the use of traditional clustering algorithms, and for which thus algorithms need to be extended/adapted. greetz, 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://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ================================================================== -- ================================================================== 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://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ==================================================================

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[Beg-sysbiol] some systems biology related papers
by Eric Bonnet 10 Nov '06

10 Nov '06

http://www.biomedcentral.com/1471-2105/7/488/abstract http://genomebiology.com/2006/7/11/R104

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[Beg-sysbiol] [Fwd: q-bio daily Subj-class mailing 2 1]
by Roeland Merks 09 Nov '06

09 Nov '06

Two network preprints. Cheers, Roeland -------- Original Message -------- Subject: q-bio daily Subj-class mailing 2 1 Date: Thu, 9 Nov 2006 05:10:04 -0500 From: no-reply(a)arXiv.org (send mail ONLY to q-bio) Reply-To: q-bio(a)arXiv.org To: rabble(a)arXiv.org (q-bio daily title/abstract distribution) ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ send mail only to q-bio(a)arXiv.org, do not reply to no-reply@... send any complaints regarding submissions directly to submitter. use a single `get' to request multiple papers, `list macros' for available macro packages, and `help' for a list of available commands and other info. ------------------------------------------------------------------------------ point your www client at http://arXiv.org/ To unsubscribe, e-mail To: q-bio(a)arXiv.org, Subject: cancel ------------------------------------------------------------------------------ Submissions to: Molecular Networks received from Tue 7 Nov 06 21:00:09 GMT to Wed 8 Nov 06 21:00:08 GMT ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ \\ Paper: q-bio.MN/0611026 Date: Tue, 7 Nov 2006 23:09:26 GMT (24kb) Title: Propagation of fluctuations in interaction networks governed by the law of mass action Authors: Sergei Maslov, Kim Sneppen, Iaroslav Ispolatov Comments: 4 pages; 2 figures Subj-class: Molecular Networks; Genomics \\ Using an example of physical interactions between proteins, we study how perturbations propagate in interconnected networks whose equilibrium state is governed by the law of mass action. We introduce a comprehensive matrix formalism which predicts the response of this equilibrium to small changes in total concentrations of individual molecules, and explain it using a heuristic analogy to a current flow in a network of resistors. Our main conclusion is that on average changes in free concentrations exponentially decay with the distance from the source of perturbation. We then study how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. An exact analytic expression for the decay constant is obtained for the case of uniform interactions on the Bethe lattice. Our general findings are illustrated using a real biological network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations. \\ ( http://arXiv.org/abs/q-bio/0611026 , 24kb) %-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%- %%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%% ------------------------------------------------------------------------------ \\ Paper: q-bio.OT/0609036 replaced with revised version Tue, 7 Nov 2006 19:51:47 GMT (415kb) Title: Using graph concepts to understand the organization of complex systems Authors: Claire Christensen and Reka Albert Comments: v(1) 38 pages, 7 figures, to appear in the International Journal of Bifurcation and Chaos v(2) Line spacing changed; now 23 pages, 7 figures, to appear in the Special Issue "Complex Networks' Structure and Dynamics'' of the International Journal of Bifurcation and Chaos (Volume 17, Issue 7, July 2007) edited by S. Boccaletti and V. Latora Subj-class: Other; Molecular Networks; Disordered Systems and Neural Networks \\ ( http://arXiv.org/abs/q-bio/0609036 , 415kb) %%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%--- -- 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] Does anyone has the pdf? Thanks, Yves
by Yves Van de Peer 07 Nov '06

07 Nov '06

http://bib.oxfordjournals.org/cgi/rapidpdf/bbl037v1

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[Beg-sysbiol] new software branch
by Tom Michoel 07 Nov '06

07 Nov '06

I created a new branch "InProgress2" which is a copy of the current frozen "Release1" and will be the playing ground for making the next generation of code changes/improvements. Do "svn update" from inside the branches directory to join the party. Tom

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