The node identifier used here is the same as that used in the interactions file above. Initial gene list: A list of the genes of interest showing their greatest change in expression in the early hours after stimulation along with their scores in the format:.The molecule name should be the same as in the gene lists. This data is currently provided in the form of a tab-delimited flat file.The reliability score is between 0 and 1.The direction of the interaction can be either "-" (bidirectional interaction) or "->" (uni-directional interaction).Molecules 1 and 2 can be an Id or a name.Input network: A list of interactions with their directionality and their reliability score in the format:.The input parameters are the same those when run on the command line. 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 lower pane displays the progress of TimeXNet. The Upper left pane is used for the input arguments.
It is necessary to specify the fully qualified path where the jar file is installed in order to run TimeXNet. Java –classpath /timexnet.jar timexnet.NetGUI The user interface can be invoked by double-clicking timexnet.jar or using the following command: TimeXNet can also be run via a user interface for a single combination of gamma1 and gamma2 values. × Single run of TimeXNet from User Interface Notice: TimeXNet Web will be temporarily affected due to Human Genome Center server maintenance until February 21 (Wednesday) 09:00 JST.
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