Cell Designer Sarah Killcoyne

Description Molecular pathway creator/editor/simulator tool (not a generic network tool)‏ Uses SBW for simulations Imports/exports via SBML Last updated January 2007 Language: Java

Plugin Architecture Will be supported in v4.0 (in alpha now)‏ Inherits from a set of classes that allow: Adding menus to popups Receiving events such as: Objects added/modified/deleted on the model Models added/modified/deleted Parameters on objects added/modified/deleted

Features Variety of layouts (most shared by Cytoscape)‏ Access to public databases such as Entrez, iHOP, etc Connection to outside tools (SBW)‏ Simulations that allow a user to watch data changing the pathway Nice, fairly intuitive GUI. Gets data via SBML or BioModels.net. Also connects to a variety of other databases including Entrez Gene and iHOP. Not really set up for generic networks. This is a pathway (molecular pathways like Kegg) creation/editor tool. It uses Sys. Bio. Workbench for a variety of functions including running simulations on models. Layouts give you some control over the parameters, acts similarly to Cytoscape in that you run a layout and wait. I don't expect CD to deal with large networks however as it is primarily a pathway tool.