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Fulden Buyukozturk

Last seen: 1 month ago |  Active since 2014

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Answered
Extracting Histogram data for plot generation
You can export the samples you generated using Model Analyzer to an Excel file: Find the samples under your program results Dr...

8 months ago | 0

Answered
save parameters after estimates as a variant in simbiology app
You can save parameter estimates as a variant by right clicking on the results and selecting Create a Variant from Estimated Par...

8 months ago | 2

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Answered
Is there a way to set UseParallel to true directly on Simbiology Model Analyzer for performing fitting with global solvers (e.g., particleswarm)?
Hi - you can do so by clicking on the Parallel icon on the top left corner of the program tab on Model Analyzer. Please see the...

12 months ago | 0

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Answered
Multiple Stages in SimBiology Model?
Hi Patrick, 1) You can use Events to implement such dicrete changes. Please see this page for details: https://www.mathworks.c...

1 year ago | 1

Answered
Can Simbiology simulate one-to-many scenarios?
You can set the stociometry of your reaction either on the Model Builder App or programmatically. On the app, you can simply mod...

1 year ago | 0

Answered
can I directly change the ODE?
You cannot edit ODEs directly but you can inspect them using getequations from the command-line or Show model equations option f...

1 year ago | 1

Answered
Drag a line to create a reaction
Hi Wenye, To connect species with a reaction, press and hold the Ctrl key (on Windows® and Linux®) or the Option key (on macOS...

2 years ago | 2

Answered
simBiology exported model simulation output not in the same order as `InitialValues`
Hello, exported_model.InitialValues lists all of exported_model's editable objects which is by default everything (compartment...

2 years ago | 1

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Answered
Space saving way to plot bar plot for sbiosobol results
Hi Jesse, You could modify properties of TiledChartLayout to save some space, such as TileSpacing. Below is an example. Oth...

2 years ago | 0

Answered
Is it possible to display initial assignments and/or parameters in SimBiology diagram?
That's right, starting R2020b initial assignments are not displayed on the diagram and only parameters that are on the left hand...

2 years ago | 0

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Answered
Question about available PK models for practicing purposes
Hi Christos, A couple of thoughts: SimBiolog has a PK library. You can pick a 1 or 2 comp model from there, populate the param...

2 years ago | 0

Answered
Visualize selected pathways in simbiology GUI
In R2022b (I understand from the release info that this is the version you're running), you can search both the Diagram and the ...

2 years ago | 0

Answered
My Matlab (version R2022b) does not include the SimBiology App by default in the App collection under the Computational Biology section
Hi, In MATLAB you can use Add-Ons Explorer to install SimBiology. Go to Home->Add-Ons->Get add-ons, seach for SimBiology and...

2 years ago | 1

Answered
How to build indirect response model?
Hi, If I understand your question correctly, your indirect response model is in derivative form as: dProtein/dt = kin - kout*(...

2 years ago | 0

Answered
How to plot individual concentration vs time plot by group?
If you have a column in your dataset with the dose info, you can use this column to slice the data using Visual Channels. Please...

2 years ago | 0

Answered
How to make simbiology plot concetratin?
SimBiology returns simulation results of quantities (for example, species) in the user specified units. So if a species is in un...

2 years ago | 0

Answered
How do I convert a BAM file to SAM and GFF file to GTF for use in featurecount?
The featurecount function now accepts BAM files. GFF is not supported by featurecount, but the cuffgffread function can convert ...

2 years ago | 0

Answered
Interested in changing line properties of sbioplot
Hello, These can be set using line object handles, for example: ax = sbioplot(sbiosimulate(m1,d)); h = findobj(ax, 'Type', '...

2 years ago | 2

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Answered
simulations of 100 samples (1 time 100 sample size) varied by Height or Weight and export data to excel file using simbiology matlab version 2022a
Hello. You could run a Scan Program to simulate with variations in weight and height. Please see this short video on how to do t...

2 years ago | 1

Answered
Is there any way to export a simbiology model diagram in high resolution?
With R2021b, you can export the diagram as a tiff, png, jpeg, etc. by selecting Export->Export Diagram on Model Builder Home tab...

3 years ago | 0

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Answered
Why do I receive an 'Invalid input argument of type 'double'. Input must be a structure or a Java or COM object' error while loading data in a simbiology fit program?
Are you running R2021b and is your dataset has only one group? If so, this is likely a known bug with the app that affects datas...

3 years ago | 0

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Answered
How can I change the compartment, species and parameter through variants?
Hi, if you choose Initial Coniditions on the home tab of Model Builder, you will see that the values on the Initial Contitions c...

3 years ago | 1

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Answered
How can i do "code capture" in Simbiology of MATLAB 2020b version?
Hi, The "code capture" tool is not available in the current version of SimBiolgy. However, you can see the MATLAB code behind ...

3 years ago | 1

Answered
Slider in Simbiology Change Range
Hi Damir, In R2021a you can just type the upper and lower range in the area below the slider and click enter. Please see belo...

3 years ago | 0

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Answered
How can I optimize parallel simulations of a SimBiology model?
Hi Colton, Yes, using SimFunction would be better as it offers easy and efficient parallelization and avoids repeated compilati...

4 years ago | 1

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Answered
Where is "RUN GROUP SIMULATION" in Simbiology Version 5.10 (R2020a)?
Hi Isabel, group simulation is no longer available starting 19b. Instead, you can create a scan program where you can input Dose...

4 years ago | 0

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Answered
Can I generate MATLAB code for a PK simulation built with SimBiology APP?
Hi Wei, If you right-click on the program on Model Analyzer and choose View program code, this will open the code for the pro...

4 years ago | 2

Answered
compartment is not being used in the model
Hi, You can ignore the "compartment is not being used in the model" warning. This warning is a benign bug with this version. S...

4 years ago | 0

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Answered
how to incorpolate various variables in simbiology model
Hi Kazutaka, You can export SimBiology model from GUI to MATLAB workspace and then use a script to add parameters. If you keep...

4 years ago | 0

| accepted

Answered
How to do model fitting in simbiology
Hello, You can "dose" Body Weight to achieve this: Set "body weight" column as a dose column - dose2 if you already have an a...

5 years ago | 1

| accepted

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