Difference between revisions of "Data availability for the manuscript"

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==Model availability and reproducibility of simulation results==
 
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===Access to the model===
 
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===Simulate the model===
 
===Simulate the model===

Revision as of 19:43, 28 May 2021

Model availability and reproducibility of simulation results

Access to the model

The modular model with all submodules as well as values of the model parameters in each module are available on BioUML web-server online (click here and use "demo" access button) or can be accessed via GitLab (click here). The model project is presented on the left side of the workspace:



  • Figure 1. The workspace of the model project in web-version of the BioUML platform. Two rectangles with red borders indicate the Trea area of the workspace and the corresponding place of the model project, respectively.



To open the integrated model or submodel diagram that is of interest, double click with the left mouse button on its icon in the Tree Area:



  • Figure 2.1. An integrated modular model linking metabolism, Ca2+-dependent signaling transduction and regulation of gene expression in human skeletal muscle (To consider the model in more details click on the figure).


  • Figure 2.2. A general SBGN diagram of the modular model describing metabolism in fibers I type taking into account metabolic processes in the cytoplasm, in the mitochondrion and transport reactions between two compartments (To consider the diagram in more details click on the figure).


  • Figure 2.3. SBGN diagram of the cytosol compartment in fibers I type representing all metabolic reactions and corresponding math equations in the module.


To consider or change the initial values of the model variables and parameter values click on the corresponding Menu Tab which is located below the diagram:



  • Figure 3.1. A Menu Tab with initial values of the model variables is highlighted by a rectangle with a red border. (To consider the model in more details click on the figure).


  • Figure 3.2. A Menu Tab with parameter values of the model is highlighted by a rectangle with a red border. (To consider the model in more details click on the figure).


Simulate the model

There are several ways to simulate the integrated model. The first one is to select the appropriate simulation engine clicking on Simulation Tab which is located below the diagram and push the Simulation button in this engine (in the rectangle with a red border):



  • Figure 4. To run the model employ Simulation tab.


The second way to reproduce simulation results presented in the manuscript is to use created Jupyter Notebook (highlighted by a rectangle with a red border) in the Trea area of the model project or launch the Notebook directly from GitLab using Binder web-service:



  • Figure 5.1. Jupyter notebook provides reproducibility of results presented in the manuscript. The notebook can be started on the BioUML server - click on the corresponding ipynb file (highlighted by a rectangle with a red border).


  • Figure 5.2. Jupyter notebook provides reproducibility of results presented in the manuscript. The notebook can be started via GitLab using Binder web-service - click on the corresponding launch icon (highlighted by a rectangle with a red border).


  • Figure 5.3. Binder allows a user to launch the Notebook in an executable environment.

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