Computational protocol: Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility

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Protocol publication

[…] The dynamical equations corresponding to the network in are given by(5) In Equation (5), the external signals to [F] and [E] are A1 and A2 respectively and the parameters values are displayed in . We did not introduce a corresponding gene X for the FOG-1 and interaction, since the PU.1–GATA-1 switch behavior is inherited by the FOG-1– mutually antagonistic network.Simulations of the differential equations were implemented using MATLAB software (The Mathworks) and the Systems Biology Workbench (SBW/BioSPICE) tools : JDesigner, and Jarnac. The bifurcation diagrams were generated using Oscill8 . […]

Pipeline specifications

Software tools SBW, Jdesigner, Oscill8
Application Mathematical modeling