Plugins_in_Development

Feel free to add your plugins in development to this list.

• The MSKCC group is developing a plugin that will allow users to view expression data on BioPAX pathways from Reactome and other databases in a more user friendly way than is currently available in Cytoscape. The goal is to allow this in 2 or 3 mouse clicks with no other actions e.g. no file editing. Contact GaryBader or EthanCerami for more information.

• I (Willem Ligtenberg, Eindhoven University of Technology, W.P.A.Ligtenberg@tue.nl) am currently developing a plugin that enables the user to extract pathway information directly from the Reactome MySQL database. At this moment it allows people to select the pathway of interst and do 2 types of colouring:

  • 1) Occurence colouring, gives the node a colour according to how many times an orthologous reaction exist in other species. (white =0, redness is amount) This currently works only for human, because of the way Reactome is created. (Human based) 2) Expression colouring, gives the node a colour according to gene expression levels. (At this moment negative foldchanges are red, positive foldchanges are green)

    It now also supports selective colouring by usage of statistical values such as the p-value. (e.g. Only colour when p-value < 0.05) The input is file format is the same as GenMAPP uses.

  A screenshot with expression colouring and PathwayFinder: Screenshot

  • User can also "grow" a pathway, by giving one PhysicalEntity, that will act as the seed for the growing proces. Then the reactions will be selected that use this PhysicalEntity as an input. Next all following reactions will be selected for viewing. The latest feature is PathwayFinder, which will create a tree with all pathways that have reactions mapped to it, that were in the Gene Expression file. (The same file that is used for expression colouring.

  I also have created an SBML importer plugin which is availble at my own website: http://www.wligtenberg.nl

• I (Richard Adams, University of Edinburgh, UK, richard.adams@ed.ac.uk) am working on a plugin for standard graph algorithms e.g., clustering coefficients, articulation points, fast APSP for non-directed graphs. Basically a class "Algorithms" with static methods called from a simple dialog window, with supporting classes for implementing traversals etc.

  • So far only undirected graphs are supported e.g., for protein interaction datasets.
• The Agilent group is developing and planning to develop several plugins over the course of 2006.

  • HyperEdge, an edge that can connect more than two nodes

  • A HeatStrips visualization, which graphically displays multiple attribute values, such as expression values, as a set of color-coded bars attached to a node

  • An AdjacencyMatrix visualization, in which nodes of a network are laid out in a rectangular grid and each row/column intersection in the grid is color-coded according to an attribute of the edge between the intersecting nodes.

  • A StencilsPlugin, which will extend the Cytoscape editor with composible patterns and motifs of multiple nodes and edges, which can be used as higher-level building blocks for networks. Stencils function similarly to macros in Microsoft Word or Excel, in that they would generate more than one node or link at a time when constructing a network. Examples of stencils include biochemical reactions, feedforward loops, and protein complexes.

  • A ColorControl widget, which enables a user to adjust, in real-time, the Node Color visual mapping, based upon an sigmoidal function that maps the range of values for a node attribute into a two-color range. Steepness and midpoint of the sigmoidal curve and threshold between the two colors can be adjusted interactively, with results immediately displayed on the current network view. The attachment TestSigmoid.avi shows an example of such a control, as implemented in an earlier Agilent prototype software tool.

  RFCs to follow. Contact AllanKuchinsky or AdityaVailaya for more information.