… ODE refers to the fact that concentration is only a function of time, not space. The advantage
of ODE-… with large number of coupled nonlinear ODEs are well developed (see Box 1). For …

… of ordinary differential equations (ODEs) describing all the changes in species concentrations
as a result of reactions or membrane transport processes. By definition, an ODE … in ODE …

… Finally, as a third formalism, Boolean networks can be transformed into logic-based ODEs
… graphs to cellular signaling networks such as the identification of signaling pathways and …

Computational models are increasingly used to analyze the operation of complex biochemical
networks, including those involved in cell signaling networks. Here we review recent …

… Virtual Cell uses two separate numerical solvers: one for their kinetic modeling that uses
Ordinary Differential Equations (ODEs) … The output of data in Virtual Cell is in different formats: …

… communication is the usage of ODE systems coupled with neural networks, which can be …
approach tailored for UDE-based cell signaling pathway modeling that consolidates these …

… cell signaling. In particular, we are interested in developing tools to characterize the qualitative
behavior of the epidermal growth factor cell signaling network. … properties of ODE models …

… for universal differential equation UDE-based cell signaling pathway modeling. The open-source…
will enable researchers to design improved cell signaling pathway models more easily, …

Protein signaling networks play a central role in … Bayesian networks, have been widely used
to model cell signaling, … observable components of signaling. Specifically, we account for …

… -induced cell death signaling [7]. This model is composed of ordinary differential equations
… Although most ODE models assume simply that the inside of cell is a mixed soup and do not …