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How can I define a time-dependent (species) reaction rate for an model in SimBiology?
Hi Puru, I would recommend you to create a reaction null -> A with a custom reaction rate defined by the quadratic equation. I...

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Is it possible to create custom (species-specific) conversion factors in Simbiology?
Hi Shalla, In this case, the easiest way is to : import your experimental data as a table add a column that divides the dose ...

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Simbiology createSimFunction data access
Hi Mohammad, the method selectbyname allows you to extract the data of a specific state. Alternatively, you can use the attach...

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Model diagram in the Simbiology freeze and disappear
(edited: added a more detailed description of the issue) Dear users, We were able to reproduce the issue you reported: Draggi...

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Simbiology dose an ode
Hi Bence, you're right, doses can't be applied to species which are defined by rate rules. Their dynamics must be defined by re...

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Model/Simulation of Drug Release in Graphical SimBio Interface
Hi Greg, we have released video tutorials which cover different topics including model building: SimBiology Tutorials for QSP,...

casi 4 años hace | 1

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setting of initial conditions simbiology
Dear Kazutaka, is this the example you are using?: PK/PD Modeling and Simulation to Guide Dosing Strategy for Antibiotics If s...

alrededor de 4 años hace | 1

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Export model to workspace - missing dose
Hi Jacopo, doses are indeed included in the model. You can retrieve them using the method getdose. getdose will return all dos...

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sbiofit example - Fit a One-Compartment Model to an Individual's PK Profile using SimBiology app
Hi Jacopo, I have had a look at your project. There were two things which differed from the programmatic example: you set the ...

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Is it possible to normalize the output using GUI?
Hi Hassan, in the SimBiology Model Analyzer App you add a step to your program to define and calculate an observable. This new...

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In Simbiology, how to graphically represent an enzyme production and its activity simultaneously?
Hi Hassan, let me try and summarize to make sure I understood your question correctly: you defined the 'flipping' reaction with...

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Dosing in sbiofit example
Hi Jacopo, this is the dose amount used to generate the synthetic data used in this example. But you are right, it should have...

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n Transit compartment in 2-compartment PK model in Simbiology
Hi Andy, I have attached a SimBiology implementation of a two compartment model with transit compartments. I hope this helps....

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How can I plot only one fitted variable after using sbiofit?
Hi Jim, thanks for this feedback. It would be a good thing to have. Have you had a look at sbiopredictionci? It computes the c...

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Is it possible to get the group (that is the subject) number in sbiofit to do a lookup?
Hi Jim, the alternative you described, which involves a subject column used as a dose for a dummy species is the best way to ge...

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Doripenem PKPD simbiology example: How to execute monte carlo simulation with off diagonal covariance values?
Hi Daniel, you're right, in this example all parameters are independent of each other. If you want to include correlations, y...

alrededor de 5 años hace | 1

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How to simulate simbiology model using array of doses?
In your code, dose_sc and dose_iv contain both all doses in your model. You should specify the name of a SC or IV dose that is ...

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Performing infusion experiment in Simbiology desktop
Hi Rajeev, whether you choose a repeated dose or a scheduled dose has rather to do with the schedule of your drug regimen. Both...

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How to create custom error model in Simbiology
Hi Praveen, the error model you suggested looks like a combined error model. But from your equation I don't see whether you exp...

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75 errors arise from simulation of Biomodels model.
The error message is pretty clear though. It says that some variables used in reaction rates are not defined. Actually the troub...

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Simulation makes no sense
By the way, I think had changed the glucose injection to 0.3 instead of 0.003 mainly to make easier to spot the event. But if y...

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Simulation makes no sense
Hi Juan Carlos, as Pax suggested in his answer to your previous question, this model does not contain units, so you can't make ...

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SimBiology getConfigSet does not recognise model object
Hi Alvaro, sbioloadproject will return a struct that contains your model(s). This should work: s = sbioloadproject('RandomNet...

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How to upload KEGG file to Simbiology so I can start analyzing.
Hi Juan Carlos, KEGG files can't be imprted into SimBiology as is. You will need to convert them into SBML files first. There ...

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In Simbiology, should the categorical variables be assigned as group variable or covariate in the dataset?
Group variable defines an index for a subject/experiment. In your dataset, ID is a group variable. Gender and age can be both co...

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Question on specifying input to sbiosimulate
Hi Deepa, there might be different reasons to get this error message. A typical one is when one of the fluxes becomes Inf or Na...

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Finding non-constant species in Simbiology Object
What you get is not a function handle but an heterogenous array of SimBiology objects. This array contains a mix of different co...

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Question on specifying input to sbiosimulate
There is multiple ways to do this: 1- if you want to run multiple simulations, I recommend to use a SimFunction that will take ...

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Output of sbiosteadystate task
See answer here.

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Accessing a variant object
Hi Deepa, you can access the variant content with the dot notation. If your variant is called v, v.Content will be an array of...

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