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

[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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[Beg-sysbiol] Interessant? Cross-species analysis of biological networks by Bayesian alignment
by Roeland Merks 17 Jul '06

17 Jul '06

Cross-species analysis of biological networks by Bayesian alignment Johannes Berg and Michael Lässig PNAS published 11 July 2006, 10.1073/pnas.0602294103 http://www.pnas.org/cgi/content/abstract/0602294103v1 <http://www.pnas.org/cgi/content/abstract/0602294103v1?etoc> ------------------------------------------------------------------------ -- 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: scripts etc Syntren]
by Tom Michoel 07 Jul '06

07 Jul '06

I put those scripts in the "java/timvdb" subdirectory of the segal project. Tom -------- Original Message -------- Subject: scripts etc Syntren Date: Fri, 07 Jul 2006 18:01:18 +0200 From: Tim Van den Bulcke <Tim.VandenBulcke(a)esat.kuleuven.be> To: tom.michoel(a)psb.ugent.be Hey Tom, hierbijgevoegd al de scripts die we overlopen hebben woensdag. Ik kon niet aan de gewijzigde genomica op de computercluster, dus ik zal Koen contacteren van zodra hij terug in Belgie is (maandag of dinsdag) daarvoor. De files: inference_Genomica_submitter.py zal jullie het meeste interesseren waarschijnlijk. Dit start een reeks genomica runs op de cluster. ./expressiondata/ bevat enkele scripts om expressiedata te genereren, misschien nog niet relevant op dit ogenblik, maar er zitten misschien een paar stukken code in die herbruikbaar zijn om dingen op een computercluster te draaien. in ./analyse/ zitten een reeks python scripts om data te verzamelen en te analyseren (ook om de output van genomica te converteren). Syntren zelf kan je afhalen op de website: http://homes.esat.kuleuven.be/~kmarchal/SynTReN/index.html Prettig weekend! Tim. -- _______________________________________________________ ir. Tim Van den Bulcke research assistant ESAT-SCD K.U. Leuven Kasteelpark Arenberg 10 B-3001 Leuven-Heverlee Belgium room: 03.11/14 tel: +32 16 32.86.43 fax: +32 16 32.19.70 email: tim.vandenbulcke(a)esat.kuleuven.be homepage: http://homes.esat.kuleuven.be/~vdbulcke/ personal homepage: http://timvandenbulcke.objectis.net _______________________________________________________

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[Beg-sysbiol] Tim VdB will visit us on wednesday
by Tom Michoel 03 Jul '06

03 Jul '06

time to be determined. tom

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