[Beg-sysbiol] cytoscape plugin demo
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/>
Ikke -----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo 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/> _______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
Ben Mahy wrote:
Ikke
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo
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
me too -- 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@psb.ugent.be http://bioinformatics.psb.ugent.be/
And me! Yves Van de Peer schreef:
Ben Mahy wrote:
Ikke
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo
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
me too
I would be interested to join. Is anyone of you planning to go to the BITS Transcriptomics Cytoscape workshop (Jan 23th) in Leuven? Klaas
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo
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
me too
_______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
For me, any time on monday or tuesday is fine. How about tuesday around 11am? Tom On 20 Dec 2008, at 11:04, Yves Van de Peer wrote:
Ben Mahy wrote:
Ikke
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo
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
me too
-- 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@psb.ugent.be
http://bioinformatics.psb.ugent.be/
_______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
-- Tom Michoel <http://www.psb.ugent.be/~tomic/>
OK Tom Michoel wrote:
For me, any time on monday or tuesday is fine. How about tuesday around 11am?
Tom
On 20 Dec 2008, at 11:04, Yves Van de Peer wrote:
Ben Mahy wrote:
Ikke
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo
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
me too
-- 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@psb.ugent.be
http://bioinformatics.psb.ugent.be/
_______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
-- Tom Michoel <http://www.psb.ugent.be/~tomic/>
_______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
Tuesday does not work for me, is it possible on Monday early afternoon? -----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Vanessa Vermeirssen Sent: zondag 21 december 2008 19:03 To: beg-sysbiol@psb.ugent.be Subject: Re: [Beg-sysbiol] cytoscape plugin demo OK Tom Michoel wrote:
For me, any time on monday or tuesday is fine. How about tuesday around 11am?
Tom
On 20 Dec 2008, at 11:04, Yves Van de Peer wrote:
Ben Mahy wrote:
Ikke
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo
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
me too
-- 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@psb.ugent.be
http://bioinformatics.psb.ugent.be/
_______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
-- Tom Michoel <http://www.psb.ugent.be/~tomic/>
_______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
_______________________________________________ Beg-sysbiol mailing list Beg-sysbiol@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol
Ben Mahy schreef:
Tuesday does not work for me, is it possible on Monday early afternoon?
Both are fine with me. Thomas
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Vanessa Vermeirssen Sent: zondag 21 december 2008 19:03 To: beg-sysbiol@psb.ugent.be Subject: Re: [Beg-sysbiol] cytoscape plugin demo
OK
Tom Michoel wrote:
For me, any time on monday or tuesday is fine. How about tuesday around 11am?
Tom
On 20 Dec 2008, at 11:04, Yves Van de Peer wrote:
Ben Mahy wrote:
Ikke
-----Original Message----- From: beg-sysbiol-bounces@psb.ugent.be [mailto:beg-sysbiol-bounces@psb.ugent.be] On Behalf Of Tom Michoel Sent: vrijdag 19 december 2008 10:38 To: beg-sysbiol@psb.ugent.be; Thomas Van Parys Subject: [Beg-sysbiol] cytoscape plugin demo
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
me too
-- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys@psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================
participants (7)
-
Ben Mahy -
Klaas Vandepoele -
Sofie Van Landeghem -
Thomas Van Parys -
Tom Michoel -
Vanessa Vermeirssen -
Yves Van de Peer