SimBiology

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Hello! I am trying to use this model "Estimating the Bioavailibility of a Drug" that I found here, to do a simultaneous fitting of my IV infusion and P.O. blood concentration time profile. I implemented a two compartment model as well. For some reason, when I am running a simulation the oral dose exhibits a bioavailbility of >= 1, even though I have the parameter F set as 0.2. I attached images of my simulation curve (green is oral dose), model diagram, ODEs, and dosing setup. I'm thinking it might have something to do with the way I set up the dosing, but please let me know if you have any advice on how I should troubleshoot this. I am using R2024a. Please let me know if I should include anything else. Thanks!

Hi! So I saved a run when I was doing fitting for my data, and put the results in a folder on the Simbiology model analzyer dashboard. I wanted to replicate that saved data but I can't seem to find where the initial parameters for that run are stored? If anyone could help or if there's any way I can further clarify please let me know!

I am using the simBiology builder app on matlab. I keep receiving an error on one of my models of a duplicate name error ( names are SSRI, SERT, 5-HT ) However, it doesn't say how to fix it. I have to models in this project and only one has this issue. How do I fix it?

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One of my colleagues wanted to send me the newest version of our Simbiology project. However everytime I download the .sbproj File it gets converted into an sbproj.zip File and I cannot open the Project as a whole in Matlab. Havent seen anyone with the same problem so I hope somebody can help me.

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!

I want to define that a specie A is being produced given by 2 degree quardratic equation as a function of time. How to define it ?

Hi As part of the US IND submission, we will have to provide the QSP model files that have been developed by a consultant using simbiology. The model files are of .sbproject format. However, when we looked at FDA acceptable formats (https://www.fda.gov/media/85816/download), they are open to accepting .m or .mat files. They have not specified the .sbproject file format. My question is have any in the community submitted .sbproject files to US FDA for the IND or NDA submissions and were accepted? If not, the next question is whether it is easy to change .sbproject files to .m or .mat format ? TIA Vinu

When I am writting a rate rule I am getting this above error message. My rule is LuxI = (1/Tx) ∗ (((tl_luxI ∗ [mRNA_luxI]) ∗ Tx) − ((dLuxI ∗ [LuxI]) ∗ Tx)) I have seen some of the error messages answers of Matlab but nothing worked in my case.Kindly help me with this.

Hi Simbiology Team: I wanted to complete a visual predictive check (VPC) following a popPK analysis using the sbionlmefitsa. I brought this up to the Simbiology team some years ago and explained that it is generally standard practice to complete a VPC following NLME population pharmacokinetics. I thought to adapt this example that used sbiofit - the nonlinear least-squares regression - for the sbionlmefitsa and it did not work: https://www.mathworks.com/help/simbio/ref/simbiology.fit.parameterconfidenceinterval.html ci = sbioparameterci(fitResults) ci_results= sbiopredictionci(ci); Plot Confidence Intervals for Model Predictions plot(ci_results) I understand there is a SimFunction tool as well. Is there way, I can simply export Simbiology results or the results as fitResults.m to do a VPC from a PopPK Example in Matlab Simbiology? Thank you.

I have an existing simbiology model that I want to control from the MATLAB command line. The documentation that I can find talks about creating new simbiology models from the MATLAB command line, but not about controlling an existing model. Help will be appreciated!

Functions to import SBML files containing function definitions into SimBiology.

Hi, I am having issues with correctly defining a rule (repeated assignment) for a block (parameter). The rule follows: [Dynamic Glucagon Secr] = kGSRd*max((-[Plasma Glu]/Vg),0) This is the only warning that I get: "Cannot perform dimensional analysis for rule 'Dynamic Glucagon Secr rule' because of the function 'max' in the rule. Because UnitConversion is on, correct simulation results will depend on this expression being dimensionally correct. Additionally, SimBiology simulates the model in a unit system determined at runtime. The units are determined by the units used in the model and the model's configset. Unless the inputs and outputs to the function are dimensionless, results may change due to configset option changes, changes to the model, or version changes in SimBiology. It is recommended that input and output arguments to functions be dimensionless to ensure correct results." Why can't I use the 'max' function? And are there any good alternatives?