Tutorials

Translation of a signalling network

Installation guides

  • Installation guide Linux
  • Download

  • Installation guide Win
  • Download

  • Installation guide OSX
  • Download



    Requirements

    To use rxncon you need also to install programs listed below

    rxncon works under Firefox 17 (IE currently not supported)
    python 2.6/2.7
    BioNetGen (required for PD and SBML)
    Perl (required for BioNetGen)
    LibSBML (required for PD)
    Cytoscape (required for regulatory graph)


    Glossary

  • Elemental reactions - change elemental states, which in turn are similar to experimental observations learn more ...
  • Contingency - is a contextual constraint on an elemental reaction. In the contingency list it is described how a target (e.g. a reaction) is affected by its effector learn more ...
  • Contingency matrix - integrates the information in the reaction and contingency lists learn more ...
  • SBGN - System Biology Graphical Notation. A standard for network visualization learn more ...
  • SBGN - PD - System Biology Graphical Notation - Process Description diagram learn more ...
  • SBGN - ER - System Biology Graphical Notation - Entity Relationship diagram learn more ...
  • SBGN - AF - System Biology Graphical Notation - Activity Flow diagram learn more ...
  • SBML - System Biology Markup Language learn more ...
  • BNGL - BioNetGen Language, used for reprezenting rule-based models learn more ...


  • Using rxncon

    To start using rxncon you first have to upload a specially formatted Excel file (only .xls is supported not .xlsx!). You can find an example/template file in the file list on this site (Example.xls).

    Creating Biographer Graphs

    If you have a local copy of rxncon running you must configure the Biographer URL. This can be

    • Online version of Biographer:
      Biographer Url: http://biographer.biologie.hu-berlin.de/
    • Local version of Biographer:
      Biographer Url: http://127.0.0.1:8000/biographer/
      The name of the application is "biographer" in this case but it depends on the name you installed the biographer web2py application under.

    Creating Cytoscape Graphs

    Make sure you have Cytoscape running with the RPC plugin activated. By pressing one of the buttons in the graph menu a graph will automatically be created in Cytoscape. To style the graph import the following Cytoscape properties file: rxncon_cytoscape.props. The following layouts correspond to each graph type:

    Full Reaction Graph -> YM: Reaction graph
    Condensed Reaction Graph -> YM: Reaction graph
    Regulatory Graph -> YM: Regulatory graph

    Creating SBML files and SBGN-PD graphs

    To create SBML files and SBGN-PD graphs you need to install BioNetGen on your computer. Ubuntu/Debian users can use the SB.OS repository to install BioNetGen.
    After you have installed BioNetGen you need to configure rxncon to find Perl and the BioNetGen script BNG2.pl.

    • Windows example:
      Perl Path: C:\Perl64\bin\perl.exe
      BioNetGen Path: C:\Program Files (x86)\BioNetGen\BNG2.pl
    • Linux example:
      Perl Path: /usr/bin/perl
      BioNetGen Path: /usr/share/bionetgen/Perl2/BNG2.pl

    This is the online and distribution version of rxncon. To get the full functionality of rxncon you will need to download this application and use it as a desktop applications.


    Network Translation


    Installation Guides


    Glossary


    Using rxncon