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

[Beg-sysbiol] cytoscape plugin demo
by Tom Michoel 22 Dec '08

22 Dec '08

Hi all, Thomas has more or less finished the cytoscape plugin for running the network motif clustering algorithms I talked about at the lunch meeting recently. What remains to be done is mainly to polish and extend the user interface, hopefully based on feedback from some of you. Who wants to see a demo and when? If you can't wait to try it, I installed a version of cytoscape with the plugin in /group/sysbiol/cytoscape-v2.6.1. Three things are important: you need to have matlab installed, set the correct library path and run cytoscape using java 1.6. On midas/tornado/smokey you're all set if you use the commands in /group/sysbiol/cytoscape-v2.6.1/motifClustHelp.txt. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] dinner with Ron Shamir
by Yves Van de Peer 14 Dec '08

14 Dec '08

Dear all, Ron Shamir and myself will have dinner Thursday night. It would be really great if you could join. Please let me know if you can/are willing to join so we can book somewhere nice. 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.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] Ron Shamir
by Yves Van de Peer 07 Dec '08

07 Dec '08

Dear all, I hope that when Ron Shamir is visiting (for the departmental lab meeting), you can find some time to talk to him, or even join for dinner (I'm thinking the first day of the meeting). Please take advantage of the fact that he is visiting. Maybe we can organize something together? 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.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] post-conference get-together?
by Tom Michoel 04 Dec '08

04 Dec '08

Sysbiol was all over the place last month, Anagha to Malaga, Nathalie & Tom to Bostom and Ying, Stephanie, Eric & Greg to Heidelbreg. Should we have a lazy friday afternoon meeting to keep each other up to date of what's going on in the rest of the world? Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] later in lab
by Vanessa Vermeirssen 04 Dec '08

04 Dec '08

Hi, I will be a bit later in today. I am working at home for the moment and have to visit the doctor later this morning. Vanessa

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[Beg-sysbiol] [Fwd: Talk on system theory and control for biochemical systems 02/12/08]
by Tom Michoel 02 Dec '08

02 Dec '08

Reminder. NB: I have no idea if this is going to be interesting or not, but I'll give them the benefit of the doubt. -------- Original Message -------- Subject: Talk on system theory and control for biochemical systems 02/12/08 Date: Tue, 18 Nov 2008 11:30:20 +0100 (Romance Standard Time) From: Jonathan Rogge <Jonathan.Rogge(a)UGent.be> To: yvpee(a)psb.ugent.be, tomic(a)psb.ugent.be, krwab(a)psb.ugent.be, willy.govaerts(a)Ugent.be, leila.kheibarshekanasl(a)ugent.be, researchers(a)systems.ugent.be CC: margot.roels(a)ugent.be Dear colleagues, I would like to inform you of a lecture taking place at the SYSTeMS Research group, titled "Problems of control and system theory for biochemical reaction systems". Speaker is prof. Jan van Schuppen, who is affiliated with the CWI and Vrije Universiteit Amsterdam. An abstract of the talk is added below. The talk will take place on December 2nd, Tuesday afternoon at 2.30pm in the classroom on the 2nd floor of building 914 at Technologiepark Zwijnaarde. Kind regards, Jonathan Rogge ======================== Problems of control and system theory for biochemical reaction systems Jan H. van Schuppen (CWI/VU University Amsterdam) Progress in the life sciences can benefit, besides experimental and descriptive research, from the mathematical sciences for modeling, system identification, system theory, and control theory. The following research issues will be discussed during the lecture: (a) Modeling of glycolysis in Trypanosoma brucei and of part of the genetic network of Escherichia coli in regard to nitrogen assimilation. (b) Biochemical reaction systems and their algebraic properties. (c) Modeling of very large biochemical reaction systems preferably of the complete cell by methods of hierarchical system theory, modularity, and algebraic decomposition. (d) System identification of rational (positive) systems. (e) System reduction of biochemical reaction systems. (f) Control for biotechnology including rational drug design and production of food substances. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] might be interesting!
by Yves Van de Peer 27 Nov '08

27 Nov '08

-------- Original Message -------- Subject: Weekly Science Meeting CANCELLED Date: Thu, 27 Nov 2008 11:54:55 +0100 From: Nathalie Vanden Hautte <nahau(a)psb.UGent.be> To: <all(a)psb.ugent.be> Dear all, *This week’s Science Meeting has been cancelled.* Tomorrow, Friday 28^th November, Jonathan M. Flowers will give a talk at 10 am in the seminar room. The title of his talk is: “Adaptation and evolutionary constraint in the evolution of genetic networks”. You can find more details on the announcement enclosed. The next Weekly Science Meeting will be held on *5^th **December 2008*** at *12:00* in the meeting room Leaf. Jeffrey Fawcett will give a talk. The title of his presentation is: /Did plants with double genomes have a better chance to survive the Cretaceous–Tertiary extinction event?/ Please find herewith the planning for the upcoming Science Meetings: 12^th December Tim Lammens 19^th December/ no talk planned: Lab Meeting /26^th December/ no talk planned: Boxing Day/ In case you are interested in giving a talk next year (starting 16^th January 2009), please let Sofie Goormachtig (sogoo(a)psb.ugent.be <mailto:sogoo@psb.ugent.be>) and me know so we can add your name to the schedule. Thank you in advance for your reply. With kind regards, For Dirk and Sofie Nathalie __________________________________________ Nathalie Vanden Hautte Administrative Assistant VIB Department of Plant Systems Biology, UGent Technologiepark 927 9052 Gent (Zwijnaarde) Belgium Tel: +32 / 9 33 13 800 Fax: +32 / 9 33 13 809 Http://www.psb.ugent.be -- 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] ice
by Eric Bonnet 25 Nov '08

25 Nov '08

I'll come later to the lab, since I'm not much of a ice-skater I'm waiting for the ice to melt... ;-) Eric

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[Beg-sysbiol] [Fwd: Talk on system theory and control for biochemical systems 02/12/08]
by Tom Michoel 18 Nov '08

18 Nov '08

-------- Original Message -------- Subject: Talk on system theory and control for biochemical systems 02/12/08 Date: Tue, 18 Nov 2008 11:30:20 +0100 (Romance Standard Time) From: Jonathan Rogge <Jonathan.Rogge(a)UGent.be> To: yvpee(a)psb.ugent.be, tomic(a)psb.ugent.be, krwab(a)psb.ugent.be, willy.govaerts(a)Ugent.be, leila.kheibarshekanasl(a)ugent.be, researchers(a)systems.ugent.be CC: margot.roels(a)ugent.be Dear colleagues, I would like to inform you of a lecture taking place at the SYSTeMS Research group, titled "Problems of control and system theory for biochemical reaction systems". Speaker is prof. Jan van Schuppen, who is affiliated with the CWI and Vrije Universiteit Amsterdam. An abstract of the talk is added below. The talk will take place on December 2nd, Tuesday afternoon at 2.30pm in the classroom on the 2nd floor of building 914 at Technologiepark Zwijnaarde. Kind regards, Jonathan Rogge ======================== Problems of control and system theory for biochemical reaction systems Jan H. van Schuppen (CWI/VU University Amsterdam) Progress in the life sciences can benefit, besides experimental and descriptive research, from the mathematical sciences for modeling, system identification, system theory, and control theory. The following research issues will be discussed during the lecture: (a) Modeling of glycolysis in Trypanosoma brucei and of part of the genetic network of Escherichia coli in regard to nitrogen assimilation. (b) Biochemical reaction systems and their algebraic properties. (c) Modeling of very large biochemical reaction systems preferably of the complete cell by methods of hierarchical system theory, modularity, and algebraic decomposition. (d) System identification of rational (positive) systems. (e) System reduction of biochemical reaction systems. (f) Control for biotechnology including rational drug design and production of food substances. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] A protocol for unraveling gene regulatory networks. [Nat Protoc. 2008] - PubMed Result
by Yves Van de Peer 16 Nov '08

16 Nov '08

http://www.ncbi.nlm.nih.gov/pubmed/19008874?dopt=Abstract -- 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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