Single run of TimeXNet from User InterfaceTimeXNet can also be run via a user interface for a single combination of gamma1 and gamma2 values. The user interface can be invoked by double-clicking timexnet.jar or using the following command: java –classpath [full installation directory]/timexnet.jar timexnet.NetGUI It is necessary to specify the fully qualified path where the jar file is installed in order to run TimeXNet. |
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User InterfaceThe Upper left pane is used for the input arguments. The lower pane displays the progress of TimeXNet. The tabbed pane on the right hand side shows two tables with the genes and edges predicted to be a part of the response network along with their flow values.
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Input parametersThe input parameters are the same those when run on the command line.
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The "Load Sample" button allows the user to load the test data and run it. | |
OutputThe lower pane displays the progress of TimeXNet. The tabbed pane on the right hand side shows two tables with the genes and edges predicted to be a part of the response network along with their flow values.
The "View Network" button allows the user to view the predicted response network in Cytoscape. TimeXNet invokes a bundled copy of Cytoscape 2.8.3 and does not require the user to install it on the user's machine.
The network nodes (genes) are color coded as follows: Red -initial response genes, Yellow -intermediate regulator, Green - late effector, Blue - predicted regulator.
TimeXNet also generates the following output files:
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Human Genome Centre, Institute of Medical Science, University of Tokyo |