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.
'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 Kullback–Leibler 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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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