Matlab 2014a Licence File 156
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We created a model of TCR signaling that simulates the regulation of TCR-proximal pTyr sites by phosphatases, kinases, and scaffolding proteins and also simulates the regulation of downstream pTyr sites by phosphatases and kinases. The model includes interactions between the components of signaling (Fig. 3 in File S1 and Fig. S7 in File S2). Among these are: 1) the existence of a “negative feedback loop” in which ZAP70 is activated by pY292 of LAT, which in turn is activated by pY292; 2) the regulated dephosphorylation of pY292 by PP2A [53]; and 3) the regulated dephosphorylation of pY292 by the SHP family of phosphatases (Fig. 3 in File S1 and Fig. S7 in File S2).
The import data process also invokes the importOptions object’s confirmImportData function in the event that the import data is inconsistent with the model’s data. The importOptions object’s validateImportData function checks the consistency of the import data and automatically invokes the model’s resolveImportData function in the event that the import data is inconsistent with the model’s data. We provide explicit comments throughout the code that explain the import data process and the workflow of our program (see supplementary information in File S1).
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One of the drawbacks to this approach was that we needed to recompile every time we made even a small change to the code. This slowed everything else we were doing down and because we couldn't always have someone waiting for the application to finish building. 827ec27edc
