July 2009 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] /group/sysbiol is almost full
by Tom Michoel 30 Jul '09

30 Jul '09

Filesystem 1K-blocks Used Available Use% Mounted on psbnas02:/vol/bioprojects/sysbiol 262144000 260809600 1334400 100% /group/sysbiol -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] Special Online Collection: Complex Systems and Networks
by Tom Michoel 30 Jul '09

30 Jul '09

http://www.sciencemag.org/complexity/

1 0

[Beg-sysbiol] Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae
by Pierre Rouze 28 Jul '09

28 Jul '09

http://www.biomedcentral.com/content/pdf/1752-0509-3-76.pdf -- Pierre ROUZE Bioinformatics / Senior Expert Scientist VIB Department of Plant Systems Biology Ghent University Technologie park 927, B-9052 GENT BELGIUM Tel :32.933 13694 Cell.Phone : 32.476 638 304 Fax :32.933 13809 pierre.rouze(a)psb.vib-ugent.be http://www.psb.ugent.be/bioinformatics ¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨ prediction is very difficult, especially about the future Niels Bohr

1 0

[Beg-sysbiol] (no subject)
by Yves Van de Peer 13 Jul '09

13 Jul '09

Dear all, I'm looking for a figure/flowchart/graph on data integration (such as metabolome proteome, transcriptome data ...). Preferably in vector format so I can change it to my needs. Thanks in advance, Yves -- 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] Methods Mol Biol. 2009;553:207-25.
by liste＠psb.vib-ugent.be 12 Jul '09

12 Jul '09

http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract… Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information. Assmann SM, Albert R. Biology Department, Penn State University, University Park, PA, USA. A major aim of systems biology is the study of the inter-relationships found within and between large biological data sets. Here we describe one systems biology method, in which the tools of network analysis and discrete dynamic (Boolean) modeling are used to develop predictive models of cellular signaling in cases where detailed temporal and kinetic information regarding the propagation of the signal through the system is lacking. This approach is also applicable to data sets derived from some other types of biological systems, such as transcription factor-mediated regulation of gene expression during the control of developmental fate, or host defense responses following pathogen attack, and is equally applicable to plant and non-plant systems. The method also allows prediction of how elimination of one or more individual signaling components will affect the ultimate outcome, thus allowing the researcher to model the effects of genetic knockout or pharmacological block. The method also serves as a starting point from which more quantitative models can be developed as additional information becomes available. L. -- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Trying is the first step towards failure." - H. Simpson

1 0

[Beg-sysbiol] [Fwd: Learning At gene functions - a challenge?]
by Yves Van de Peer 09 Jul '09

09 Jul '09

-------- Original Message -------- Subject: Learning At gene functions - a challenge? Date: Wed, 24 Jun 2009 14:35:16 +0100 From: Andrew Millar <Andrew.Millar(a)ed.ac.uk> To: schoof(a)mpiz-koeln.mpg.de <schoof(a)mpiz-koeln.mpg.de>, rodrigo.gutierrez(a)gmail.com <rodrigo.gutierrez(a)gmail.com> CC: cdtown(a)jcvi.org <cdtown(a)jcvi.org>, flegeai(a)infobiogen.fr <flegeai(a)infobiogen.fr>, yvdp(a)psb.UGent.be <yvdp(a)psb.UGent.be>, yn(a)kazusa.or.jp <yn(a)kazusa.or.jp>, philip.benfey(a)duke.edu <philip.benfey(a)duke.edu>, mash(a)iastate.edu <mash(a)iastate.edu>, Wilhelm Gruissem <wgruissem(a)ethz.ch> Dear MASC BI and SysBio members, I have just met Quaid Morris, machine learning PI from U Toronto. Nick Provart has clearly done a great job of selling Arabidopsis to him. Quaid talked about the 'MouseFunc challenge' for assigning gene functions based on machine learning from genomic data sets. With a broad-scale At interactome coming up soon, I asked if this was somethign the A.t. community could consider, and he reacted very positively. I know that at least some of Olga Tronskaya's lab are also interested in plants, and Insuk Lee from Ed Marcotte's lab has been developing his FunctionalNet for Arabidopsis. Hence there is enough interest from that community. Apologies in advance if this is something you have already considered. If not, maybe we could discuss at the upcoming meeting? http://hugheslab.med.utoronto.ca/supplementary-data/mouseFunc_I/ has the details. The key ingredients were: - a 'host' lab to establish the challenge; a potential conflict was that the host also participated as a contestant - we might avoid that. - Genome Biology journal was lined up to publish a paper on the challenge and papers on the best results - they had a professional annotator to look at the consensus of the best networks and comment on it. We might get the consensus published as well as the individual efforts. Also, theirs was by invitation only, we could be more open and international. Best regards, Andrew -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] Article series : Nature Reviews Genetics
by Yves Van de Peer 08 Jul '09

08 Jul '09

http://www.nature.com/nrg/series/modelling/index.html -- 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] [Fwd: DREAM4 Predictive Signaling Network Modeling Challenge Added]
by Tom Michoel 03 Jul '09

03 Jul '09

This one looks quite interesting. Tom -------- Original Message -------- Subject: DREAM4 Predictive Signaling Network Modeling Challenge Added Date: Thu, 2 Jul 2009 20:31:02 -0400 From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> To: DREAM N-Z <DREAM_N-Z%IBMUS(a)us.ibm.com> PLEASE LET ME KNOW IF YOU PREFER NOT TO RECEIVE ANNOUNCEMENTS FROM THE DREAM PROJECT SINCERE APOLOGIES IF YOU RECEIVE THIS ANNOUNCEMENT MORE THAN ONCE * **New (and last) Network Inference Challenge Posted: Predictive Signaling Network Modeling Challenge ** DREAM4: The 4^th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS* Dear Colleague, We would like to alert you that the last challenge (Challenge 3) that completes the series of 3 challenges for DREAM4 has just been posted on our website. Please take a look at: http://wiki.c2b2.columbia.edu/dream/index.php/D4c3 for the challenge description. We would like to cordially invite your submissions to this new biological prediction challenge. To access the data sets, and descriptions of the challenges, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/Challenges_ . The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM4 conference. See _http://compbio.mit.edu/recombsat/_ for details on this conference. To learn more about the DREAM4 conference, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/DREAM4conf_ To learn more about the DREAM project, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project_ * Predictive Network Modeling Submission Timeline* * Oct 15, 2009* Predictions Submission Deadline. * Nov 15, 2009* Notifications to Predictors of their Scores and Ranks.* Dec 2-Dec 6, 2009* RECOMB Systems Biology/Regulatory Genomics/DREAM4 conference. (The DREAM4 conference track is on Friday December 4th.) Prediction Submissions must be received in electronic form by 11:59pm (EST) of October 15, 2009. *PLEASE FORWARD THIS NOTICE TO OTHER COLLEAGUES THAT MAY BE INTERESTED IN PARTICIPATING IN THE CHALLENGES*. Sincerely, DREAM4 Conference and Challenge Organizers: Gustavo Stolovitzky (chair), IBM Research Robert J Prill, IBM Research Andrea Califano, Columbia University DREAM4 is part of a project we call the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. Its main objective is to catalyze the interaction between experiment and theory in the area of cellular network inference. The fundamental question for DREAM is simple: How can researchers assess how well they are describing the networks of interacting molecules that underlie biological systems, and how well can they predict the results of a biological experiment? The answer is not so simple. Researchers have used a variety of algorithms to deduce the structure of very different biological and artificial networks, and evaluated their success using various metrics. What is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of the methods and a clear sense of the reliability of the network models they produce. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0