1. Modeling patterns of p53 activation dynamics from natural language
Modeling patterns of p53 activation dynamics from natural language Patterns of p53 activation dynamics upon double‐strand break DNA damage (left) and single‐strand break DNA damage (right), adapted from Purvis and Lahav (2013). Edges with yellow numbers correspond to the original diagram in Purvis and Lahav (2013); pink and green numbers correspond to mechanisms added subsequently, as described in the text.Natural language descriptions of the mechanisms involved in single‐strand break DNA damage (SSB) response corresponding to the diagram on the left‐hand side of (A) and dynamical simulation of p53 activity from the corresponding INDRA‐assembled model (below).Natural language descriptions of the mechanisms involved in double‐strand break DNA damage (DSB) response corresponding to the diagram on the right‐hand side of (A) and dynamical simulation of p53 activity from the corresponding INDRA‐assembled model (below).For the base sentence “Wip1 inactivates ATM”, variants in the names of entities are shown below with four examples that produce the intended result (green sidebar) and one example that does not (red sidebar). To the right, eleven linguistic variants of the sentence are shown with eight producing the intended result (green sidebar) and three that do not, including one with a grammatical error and one with a spelling error (red sidebar).The POMI1.0 model is a mechanistically more detailed variant of the double‐strand break response model (which is shown in the right‐hand side diagram of A, with its natural language description shown in B). The model assembled with INDRA produces oscillations in p53 activity over time when simulated (bottom).
Benjamin M Gyori et al. Mol Syst Biol 2017;13:954
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