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

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

06 Aug '06

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

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

06 Aug '06

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

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[Beg-sysbiol] svn branch
by Eric Bonnet 04 Aug '06

04 Aug '06

Hi there, We've created a branch for our project in the svn system. The idea is to work on a "release" version of the code that will be published together with the paper, slightly more polished and without unnecessary options. So after a svn update or checkout you should find a dir Release1 in the "branch" svn directory, next to the "trunk" who is containing the main version. - The new realease adopt the standard java naming convention: new package name is be.ugent.psb.ModuleNetwork - I created a "parameter file" system: the program is looking in the current directory for a file named "ModuleNetwork.par" text file containing all the necessary parameters in the form variable_name=value eg lambda0=0.1. The file can also be given on the command line as an argument. I've put an example in segal/java/test_data. Voila ! Eric

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[Beg-sysbiol] outline BMC paper
by Tom Michoel 03 Aug '06

03 Aug '06

Hello, I wrote down a trial outline for our paper. Maybe we can discuss this as well as some new results sometime tomorrow? Tom

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[Beg-sysbiol] Inferring models of gene expression dynamics [for Arabidopsis floral morphogenesis]
by Roeland Merks 03 Aug '06

03 Aug '06

Hi all, Have seen this paper? (See attachment). Cheers, Roeland -- 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] discussion syntren paper tomorrow ?
by Steven Maere 31 Jul '06

31 Jul '06

Hi all, I'm back from holidays (and it was fun) ! Could we perhaps meet tomorrow on the syntren paper, so that I can get up to speed ? What about 14.00 ? 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] Dry work in a wet world: computation in systems biology : Molecular Systems Biology
by Yves Van de Peer 27 Jul '06

27 Jul '06

http://www.nature.com/msb/journal/v2/n1/full/msb4100080.html

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[Beg-sysbiol] Maybe someone - should go? Let's discuss this?
by Yves Van de Peer 26 Jul '06

26 Jul '06

http://www-db.embl.de/jss/EmblGroupsOrg/conf_36#t_2_0

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[Beg-sysbiol] Systems Biology Channel | New York Academy of Sciences
by Yves Van de Peer 26 Jul '06

26 Jul '06

http://www.nyas.org/channels/index.asp?channelID=34

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[Beg-sysbiol] BioSystems special issue on Modeling of Biological Regulatory Networks
by Roeland Merks 17 Jul '06

17 Jul '06

Cheers, Roeland -------- Original Message -------- Subject: ContentsDirect - BioSystems, Vol 84 Iss 2 Date: Sun, 7 May 2006 10:45:45 +0100 (BST) From: cdmailer(a)elsevier.co.uk Reply-To: cdmailer(a)elsevier.co.uk To: <cdarchive(a)elsevier.co.uk> (ContentsDirect - BioSystems, Vol 84 Iss 2) ContentsDirect from Elsevier ______________________________________________________ The ContentsDirect e-mail alerting service will close on the 25 May 2006. If you wish to continue to receive journal and book alerts from Elsevier after this date please click this link to find out about alternative services http://contentsdirect.elsevier.com ______________________________________________________ Journal: BioSystems ISSN : 0303-2647 Volume : 84 Issue : 2 [SPECIAL ISSUE] Date : May-2006 Selected Papers from Workshop at Dynamical Modeling of Biological Regulatory Networks ICSB 2004 2004/04 Edited by: Hidde de Jonge, Claudine Chaouiya, Denis Thieffry For more information about this journal visit: http://www.elsevier.com/locate/biosystems ______________________________________________________ If you are interested in submitting a paper to this journal visit: http://authors.elsevier.com/journal/biosystems ______________________________________________________ Table of Contents: IFC (Ed. Board) pp CO2 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… Special Issue Contents pp v Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… Dynamical modeling of biological regulatory networks C. Chaouiya, H. de Jong, D. Thieffry pp 77-80 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… An analysis of the class of gene regulatory functions implied by a biochemical model J. Grefenstette, S. Kim, S. Kauffman pp 81-90 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks A.G. Gonzalez, A. Naldi, L. Sanchez, D. Thieffry, C. Chaouiya pp 91-100 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… A network model for the control of the differentiation process in Th cells L. Mendoza pp 101-114 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… Dynamical properties of model gene networks and implications for the inverse problem T.J. Perkins, M. Hallett, L. Glass pp 115-123 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… Qualitative simulation of the carbon starvation response in Escherichia coli D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann pp 124-152 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks A. Siegel, O. Radulescu, M. Le Borgne, P. Veber, J. Ouy, S. Lagarrigue pp 153-174 Full text via ScienceDirect : http://www.sciencedirect.com/science?_ob=GatewayURL&_origin=CONTENTS&_metho… ----------------------------------------------------------------------BioSystems Impact Factor Now: 1.016 ******************************************* A list with the most downloaded articles for this journal can be found at: http://top25.sciencedirect.com For top downloaded papers of other Elsevier journals browse the journal homepage at: www.elsevier.com ---------------------------------------------------------------------- ______________________________________________________ Full Text available via ScienceDirect: ScienceDirect (http://www.sciencedirect.com) provides subscribers with online access to the full text of more than 1,800 journals. If your institute does not subscribe to the journal you are interested in, ScienceDirect offers you the possibility to pay per article. 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Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior written permission of Elsevier Limited. No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Users should take note that information contained in ContentsDirect for journals is pre-publication and may well be revised or modified in future. -- 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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