http://groups.google.com/group/bionetbuilder BioNetBuilder is a plugin for Cytoscape which builds biological interactions networks. This group is for discussion, technical help, feature requests and other announcements about BioNetBuilder. 2009-11-22T17:26:51Z Google Groups Jay Konieczka jkoniec...@mcb.harvard.edu 2009-11-22T17:26:51Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/4c488d968d2e627b/31ea588a02cd62d1?show_docid=31ea588a02cd62d1

Hi Gabriel, <br> <p>The first thing to check is to make sure you're online. If that's all <br> ok and you still get this error. Try reinstalling the plugin using <br> the plugin manager in cytoscape to first delete it, then reinstall. <br> Let us know if you're still having trouble. <br> <p>Jay <br> <p>-- <br> Jay H. Konieczka

Gabriel Lazcano gabriel_lazc...@hotmail.com 2009-11-22T00:01:02Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/4c488d968d2e627b/cbc09ba2ef85c833?show_docid=cbc09ba2ef85c833

Hi, <br> <p>I am experiencing problems with BioNetBuilder in Cytoscape. Actually, last week I was able to use it and now I have the following error <br> <p>“Ugg. Sorry for the trouble, We were unable to create BioNetBuilder Wizard. Please let us know about this at bionetbuilder@googlegroups” <br> <p>Any clue about it ?

Patrick Winters patrick.wint...@gmail.com 2009-11-06T16:23:24Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/9126f4f1d1d0175a/3ce58aca17051f2f?show_docid=3ce58aca17051f2f

Heather, <br> We apologize for disrupting your demonstration. We recently updated <br> our interaction databases and have noticed our server struggling with <br> memory issues. The databases and queries have outgrown our memory <br> settings for BioNetBuilder, but I've increased their limits and will <br> make sure we upgrade the hardware soon. The server has been

Jay Konieczka jkoniec...@mcb.harvard.edu 2009-11-06T15:57:36Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/bd5a03e9a0688440/56af777bd8952492?show_docid=56af777bd8952492

Hi Dee, <br> <p>I'm confused. Is this a new list and a new problem? What would you <br> like me to do? <br> <p>Jay

Dee derin...@hotmail.com 2009-10-29T18:31:57Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/bd5a03e9a0688440/30d8a9267d54b4d8?show_docid=30d8a9267d54b4d8

Hi Jay, <br> <p>Here is the list. <br> <p>RefSeq:NM_001001881 <br> RefSeq:NM_001001932 <br> RefSeq:NM_001002268 <br> RefSeq:NM_001002927 <br> RefSeq:NM_001003948 <br> RefSeq:NM_025483 <br> RefSeq:NM_001005508 <br> RefSeq:NM_178902 <br> RefSeq:NM_029334 <br> RefSeq:NM_023118 <br> RefSeq:NM_023118 <br> RefSeq:NM_001012401 <br> RefSeq:NM_001013028 <br> RefSeq:NM_001013371

heather heather.vinc...@manchester.ac.uk 2009-11-06T14:49:11Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/9126f4f1d1d0175a/0841374926a334e2?show_docid=0841374926a334e2

This morning, UK time, I was demonstrating BioNetBuilder to a group of <br> students. It was fine at first, but then we started getting 'We were <br> unable to set interaction sources on the server'. I hope that we <br> have not overloaded your server ;-( <br> <p>Thanks <br> <p>Heather

Dee derin...@hotmail.com 2009-10-29T18:34:39Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/bd5a03e9a0688440/b1ac8e7ac5221442?show_docid=b1ac8e7ac5221442

Hi Jay, <br> I am not sure if i added to the thread correctly but here is the list <br> again: <br> <p>RefSeq:NM_001001881 <br> RefSeq:NM_001001932 <br> RefSeq:NM_001002268 <br> RefSeq:NM_001002927 <br> RefSeq:NM_001003948 <br> RefSeq:NM_025483 <br> RefSeq:NM_001005508 <br> RefSeq:NM_178902 <br> RefSeq:NM_029334 <br> RefSeq:NM_023118 <br> RefSeq:NM_023118

Richard Bonneau bonn...@nyu.edu 2009-11-04T18:36:23Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/7441ae6b77d8d57f/e691ddbc9b101c18?show_docid=e691ddbc9b101c18

Begin forwarded message:

Jay Konieczka jkoniec...@mcb.harvard.edu 2009-10-29T01:05:03Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/bd5a03e9a0688440/f55e986910efac3c?show_docid=f55e986910efac3c

Hi Dee, <br> <p>Can you send me the list so I can take a look? <br> <p>Thanks, <br> <p>Jay <br> <p>-- <br> Jay H. Konieczka <br> Postdoctoral Fellow <br> <p>O'Shea Lab <br> Harvard University <br> Northwest Labs <br> 52 Oxford Street, Room 440 <br> Cambridge, MA 02138 <br> <p>Regev Lab <br> Broad Institute <br> 7 Cambridge Center <br> NE30-6175U

Kevin Drew kd...@nyu.edu 2009-10-28T22:13:54Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/34acb7d05086c3d6/17a927184a2212b1?show_docid=17a927184a2212b1

Hi, <br> This depends on the level of detail you are interested in. We have <br> several publications on BioNetBuilder but they are generally limited <br> to a page or two so are not very detailed. The other way is to dive <br> into the code which can be checked out anonymously from the website. <br> This maybe too much detail.

derin...@hotmail.com 2009-10-28T21:53:54Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/bd5a03e9a0688440/c5ee104dd55d76d9?show_docid=c5ee104dd55d76d9

Hi, <br> <p>I have been trying to build a network from a list of nodes (~500). i <br> go through the steps without a problem but the network that is <br> generated has over 3000 nodes in it (even when i do not ask the <br> program to include nearest neighbour nodes!). <br> As a test i tried to make a network with only 6 input nodes. it still

Kevin Drew kd...@nyu.edu 2009-10-27T00:33:11Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/34acb7d05086c3d6/9d8145d800e6a990?show_docid=9d8145d800e6a990

Hi, <br> Thanks for the heads up. I just recycled the server. Please let me <br> know if you are still having problems. <br> Also, we have a google groups where you might get a quicker response <br> with questions. <br> <a target="_blank" rel=nofollow href="http://groups.google.com/group/bionetbuilder?hl=en">[link]</a> <br> Thanks, <br> Kevin

Jay Konieczka jkoniec...@mcb.harvard.edu 2009-10-13T22:31:42Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/90458802f1d31fa3/c555b24c79457ae9?show_docid=c555b24c79457ae9

Hi Xianyao, <br> <p>I just installed the BioNetBuilder plugin into Cytoscape version 2.6.3 <br> on a Mac running OSX 10.5.9 using the plugin manager and it started <br> correctly. If you are not already using Cytoscape 2.6.3, please <br> upgrade to this version. Then try using the plugin manager to delete

lxylly lxy...@gmail.com 2009-10-13T22:05:50Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/90458802f1d31fa3/e62850738143bff3?show_docid=e62850738143bff3

I try to follow up the paper in BMC 2009, 10. <br> <p>I did through plug-in manager and download the plugin to plugins <br> folder inside Cytoscape. <br> <p>The error message showed We were unable to creat BioNetBuilder wizard. <br> <p>What is wrong with that? Thanks <br> <p>Xianyao

baban sanjuktade...@gmail.com 2009-10-08T07:56:57Z http://groups.google.com/group/bionetbuilder/browse_frm/thread/db62b1b5c3b646b4/dc3dc38bac895a23?show_docid=dc3dc38bac895a23

Hello! <br> I`ve found the error stating that U found a bug in the node <br> source panel.Please send us an email to let us know what you are <br> doing. <br> Well, I have been trying to build a network of the genes we have <br> identified in our lab using hits from Arabidopsis. Once the GI list <br> (generated in notepad and worked on before on Cytoscape) is being