The network/circuit to be simulated can be specified here. There are multiple ways to do so. As an example, we have loaded the canonical toggle switch circuit as the default circuit. It can be modified either by loading the circuit from a file containing three columns, 'Source', 'Target', 'Interaction' (1 - activation, 2 - inhibition ) separated by space and each row specifying an interaction. One can also 'add', 'delete', 'undo delete' interactions in the table below. Clicking the 'Load Circuit' button will load the circuit and display it in the right panel. Database tab can be used to specify a circuit if one of the circuits from the database is to be loaded. Use 'Circuit Name' to provide a specific name to your circuit. 'Download Circuit' will download the loaded circuit as a text file.

Download Circuit







'GeneVyuha' tab simulates a circuit with a specific parameter set. Once the circuit is loaded from the 'Circuit' or 'Database' tab, a random set of parameters is generated. If the circuit from the database has its own parameter set, that set is used. The parameter set contains two paramters for each gene and three parameters for each interactions. The gene parameters are production (G_'gene') and degradation (k_'gene') rate whereas the parameters for each interaction ('source'_'target') are 'threshold' (TH_), 'hill coefficient of cooperativity' and 'fold change'. These parameters can be modified using the dropdown box given below. The default value of the parameter is dispalyed when a parameter is selected. Edit the 'value' and click 'Update' to modify this value. Repeat these steps if other parameters are to be modified. Other simulation paramters can also be modified.


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One can compare the simulated expression with other simulated or experimental expression. The simulated expression can be uploaded from a file or from the RACIPE tab. The reference data is clustered into the specified number of clusters. Then each simulated data sample is compared with each sample of the cluster to find the cluster most similar to its expression pattern. Gene permutation is used to generate the null hypothesis. The percentage of samples belonging to each cluster in the reference and simulated expressions as well as the overall KullbackÔÇôLeibler divergence between the two distributions is reported. Heatmaps of both simulated and reference expressions as well as sample-sample correaltion is also plotted. Cluster 0 is the null cluster and by default we add one sample belonging to null cluster to the reference samples
Upload Experimental Data (.csv)
Upload Simulated Data (.csv)
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Download Data




The development of the web-app is supported by a startup fund from The Jackson Laboratory and by the National Institutes of Health under Award Number [P30CA034196] and [R35GM128717]. Work at the the Center for Theoretical Biological Physics sponsored by the National Science Foundation NSF Grant PHY-1427654.


Please report any feature requests, bugs or concerns to Vivek Kohar, vivek.kohar@jax.org and Mingyang Lu, mingyang.lu@jax.org