CellDesigner also provides the possibility to simulate temporal dynamics of the gene regulatory network due to the integration of the SBML ODE (ordinary differential equation) solver.
Since each signaling component of the network can be only in two different states, boolean modeling cannot simulate temporal dynamics of protein concentrations.
We virtually delete each of the five genes from the wild type model and simulate temporal dynamics of proteins in these knockout models (Additional file 2: Tables S1, S2, S3, S4 and S5, Figures S1, S2, S3, S4 and S5).
Using this approach, the TNFR1 model was extended to simulate the temporal dynamics of groups I, II and III genes.
So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms.
Finally, challenging the model with a simulated temporal profile of Gli activity, which mimics the in vivo dynamics of Gli activity, produced the experimentally observed gene expression outputs.
The combination model of cellular automata and multi-agent system were used in this paper for simulating spatio-temporal dynamics of urban expansion and its encroachment on other lands at the regional scale.
However, a correct reproduction of river discharge by hydrological models does not guarantee the adequacy of simulated spatio-temporal dynamics of soil moisture, water fluxes and groundwater in the basin.
Through parameter fitting of measured autophagy activities we were able to accurately simulate spatio-temporal dynamics of basal and activated autophagic flux.
Huangpi, a suburban area in Wuhan, is utilized as the case study area to simulate the spatial and temporal dynamics of urban growth from 2004 to 2024.
This paper presents an integrative conceptual framework developed to simulate the spatial and temporal dynamics of water demand caused by human influences and climate change, at the river basin management scale.
