SimBiology

Segui

I have both Simbiology and MATLAB installed on my machine. I have implemented a SimBiology model using MATLAB code, which is saved as a .m file. I would like to save or convert this model to a .sbproj file. Is there a way to achieve this? I am trying to do this because we simulate our model using a MATLAB script. This script defines all of the modeling parameters, including an SSA solver and triggering events. Our previous model was implemented using the SimBiology Graphical User Interface. We have made a similar model using SimBiology Command Line. The model we created is somewhat similar to what is shown here: https://www.mathworks.com/help/simbio/gs/-model-a-gene-regulation-pathway.html. We want to simulate the new model that was created from the SimBiology Command Line using our simulation script. However, this requires the SimBiology model to be saved in .sbproj format. Any ideas on how this could be achieved would be much appreciated. Thank you!

Simbiology Desktop shows the ODEs in terms of fluxes. This script substitutes the flux values in to ODEs and prints the ODEs to screen.

This tool pulls the reaction rates out of your SimBiology model.

hello, I have some questions regarding to plotting a graph after simulating a model. 1. Is there a way to combine multiple species and consider them as one hypothetical specie? Let's say I created a model using the following reactions, and then run a simulation, and plot a graph. ProteinA + Mg -> ProteinA_Mg ProteinA_Mg + Mg -> ProteinA_Mg_Mg If I want to plot a graph with only two species (Mg and ProteinA_with_any_number_of_Mg_molecules_attached), how could I accomplish this task? 2. Also, when creating a model w/out specifying the units (InitialAmountUnits and units for reaction rate constants), what unit is used by default? Thanks in advance, Molly