Overview
SQUAD is a software for the dynamic modelling of regulatory networks using the Standardized Qualitative Approach published by Mendoza and Xenarios. The software is described in Di Cara et al., 2007.
Our method has three novel aspects with respect to other approaches. First, the user needs to provide only the connectivity of a regulatory network; no rate values, interaction strengths, or kinetic data is needed as input. Second, the stable steady states of activation of the continuous model are automatically found, without the need of running the system from several initial states. And third, the resulting equations have diverse tunable parameters so as to provide the possibility to fit the continuous model to existing experimental data. The algorithm behind SQUAD has already been shown to correctly describe the qualitative behavior of a large regulatory network.
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DOWNLOAD SQUAD (v2.0), Requires: JAVA 1.6 or above.
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Look at the TUTORIAL for help.
Quick start
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Create an empty directory and locate the Squad2.zip file in there.
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Unzip Squad2.zip.
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Type chmod +x Squad2 and run it (Linux), or click on Squad2.bat (Windows).
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To load a file, click on Load Network and select the THelper_network.xml file from the embedded samples folder.
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To identify the steady states of the network, click on Run Analysis, the steady stes identified will appear in the following panel.
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To perform the dynamic simulation, click on Initialize and then Run, you will see a plot with the results of the simulation.
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The initial values for the simulation can be edited through the nodes table or by selecting another initial steady-state with the Load State button.
Dynamic study of the T helper cell regulatory network subject to IL-4 and interferon-γ treatment.
