http://gaggle.systemsbiology.org/wiki/ 2008-07-14T13:28:41+01:00 http://gaggle.systemsbiology.org/wiki/ http://gaggle.systemsbiology.org/wiki/lib/images/favicon.ico text/html 2008-07-14T11:31:37+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=firegoose_website_handlers&do=diff1216060297 A website handler is a chunk of javascript that can transfer data from the gaggle to a given website, or back the other way. The code below (websiteHandler.js) shows the interface that a website handler needs to implement. This handler registers an ... text/html 2008-05-01T09:51:27+01:00 anonymous@10.10.2.164 http://gaggle.systemsbiology.org/wiki/doku.php?id=workshop&do=diff1209660687 Dates: August 25-26, 2008 Location: Institute for Systems Biology, Seattle, WA The 2nd Gaggle workshop will be held at the Institute for Systems Biology in Seattle, Washington in August of 2008. Topics: Visualization and analysis Data managemen... text/html 2008-04-11T16:14:54+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=firegoose_api&do=diff1207955694 A page to hash out preliminary ideas for an API that would allow gaggle-like communication between javascripted web pages (GWT or otherwise) using Firegoose as an intermediary. Note The notation x: String means a variable x of type String. Existi... text/html 2008-04-11T14:35:12+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=firegoose&do=diff1207949712 The FireGoose is a Mozilla Firefox extension that connects Firefox to the Gaggle. firegoose planned features firegoose_website_handlers firegoose bugs Firegoose Development Firegoose API Technologies XUL, javascript, XPCOM, Java, and RMI. ... text/html 2008-04-10T16:52:13+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=applications_to_research&do=diff1207871533 Examples of how the Gaggle and related software tools can be applied to systems biology research. ... text/html 2008-04-10T16:50:26+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=visualization_and_analysis&do=diff1207871426 Visualization and Analysis R and Bioconductor MeV - Multiexperiment Viewer Genome Browser ... text/html 2008-04-10T16:48:36+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=data_management&do=diff1207871316 Data Management ... text/html 2008-04-10T16:48:10+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=messaging_architecture&do=diff1207871290 Messaging Architectures Mule ... text/html 2008-04-10T16:44:04+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=workshop_agenda_2007&do=diff1207871044 Gaggle Workshop 2007 Agenda Tools Visualization Cytoscape: Networks BioTapestry: regulatory circuits Genome viewer / browser Databases & data management BioNet-Builder BRM: Bioinformatics Resource Manager Firegoose: Firefox toolb... text/html 2007-12-27T11:53:32+01:00 anonymous@10.10.2.164 http://gaggle.systemsbiology.org/wiki/doku.php?id=gwap&do=diff1198785212 The GWAP is the next step in the evolution of the Gaggle. It is currently under development, and not publicly available. The GWAP allows persistence of Gaggle data in a Web 2.0 framework. The GWAP is a collaboration between the Aebersold and B... text/html 2007-12-21T17:51:36+01:00 anonymous@10.10.2.164 http://gaggle.systemsbiology.org/wiki/doku.php?id=start&do=diff1198288296 This is a wiki for the Gaggle software. Documentation R build and install tips Data Repositories Development Gaggle Development Gaggle Data Management Proposed Refactoring: DataLoader, data repositories, and DMV Firegoose Egrin Genome B... text/html 2007-12-19T21:09:53+01:00 anonymous@216.9.11.36 http://gaggle.systemsbiology.org/wiki/doku.php?id=noncoding_rnas&do=diff1198127393 http://dx.doi.org/10.1016/j.ygeno.2004.10.005 http://www.genome.org/cgi/content/abstract/17/10/1471 http://genomebiology.com/2007/8/11/R239 ... text/html 2007-12-19T21:01:52+01:00 anonymous@216.9.11.36 http://gaggle.systemsbiology.org/wiki/doku.php?id=genome_browser_development&do=diff1198126912 One purpose of the Genome Browser is to find noncoding RNAs. Features in Progress (as of 2007-10-30) fix odd behavior of chromosome menu fix track loading progress bar draw markers at the center of all features reload datasets bookmark segm... text/html 2007-11-01T11:16:27+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=firegoose_planned_features&do=diff1193940987 Features related to the DAVID functional annotation tool. better defaulting (of ID types to GI) broadcast functional clusters back to the Gaggle (more easily) Protein complexes how to represent a small handful of proteins that form a complex ... text/html 2007-10-31T14:59:05+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=links&do=diff1193867945 Geese MeV: MultiExperiment Viewer Cytoscape BioTapestry BRM at PNNL String: functional protein association networks KEGG: Kyoto Encyclopedia of Genes and Genomes DAVID: functional annotation tools Software Systems Biology Workbench The ... text/html 2007-10-25T14:51:30+01:00 anonymous@10.10.2.164 http://gaggle.systemsbiology.org/wiki/doku.php?id=stable_urls&do=diff1193349090 These URLs are referenced in papers of from other websites and should remain stable. TODO: Authors of papers should add to this page the URLs references in their papers. URL Referenced from http://gaggle.systemsbiology.net ... text/html 2007-10-25T14:49:15+01:00 anonymous@10.10.2.164 http://gaggle.systemsbiology.org/wiki/doku.php?id=principles&do=diff1193348955 Gaggle Development Principles Core components The core components of the Gaggle are the Boss and the Goose interfaces. Because all Geese depend on these interfaces, changes to them require changes to all Geese. Therefore, changes to these interfa... text/html 2007-10-25T12:19:00+01:00 anonymous@10.10.2.164 http://gaggle.systemsbiology.org/wiki/doku.php?id=rbuildandinstall&do=diff1193339940 In the top level of the gaggle codebase, type "ant r-jar" cd org/systemsbiology/gaggle/geese/rShell cd org/systemsbiology/gaggle/geese/scripts/r/gagglePackage make build (if you are preparing for a release): make check ... text/html 2007-10-25T11:27:48+01:00 anonymous@10.10.4.241 http://gaggle.systemsbiology.org/wiki/doku.php?id=firegoose_development&do=diff1193336868 Getting set up to develop en extension involves creating a dev profile, tweaking some debuggin settings in firefox, and installing a couple of extensions that will help a lot. Instructions are here: Setting up extension development environment Here... text/html 2007-10-16T23:11:30+01:00 anonymous@206.124.153.155 http://gaggle.systemsbiology.org/wiki/doku.php?id=egrin&do=diff1192601490 EGRIN is a viewer for biclusters generated by CMonkey and regulatory networks generated by Inferelator. To do wildcard search DB back end launch BioTapestry given a list of genes, search for regulators ...