Data availability for the manuscript - Revision history

Akberdinir@gmail.com: /* Model availability and reproducibility of simulation results */

2021-06-01T08:55:05Z

‎Model availability and reproducibility of simulation results

Akberdinir@gmail.com: /* Model availability and reproducibility of simulation results */

2021-05-28T12:48:43Z

‎Model availability and reproducibility of simulation results

Akberdinir@gmail.com: /* Model availability and reproducibility of simulation results */

2021-05-28T12:43:39Z

‎Model availability and reproducibility of simulation results

Akberdinir@gmail.com: /* Model availability and reproduction of simulation results */

2021-05-28T12:40:32Z

‎Model availability and reproduction of simulation results

Akberdinir@gmail.com: /* Model availability and reproduction of simulation results */

2021-05-28T12:06:03Z

‎Model availability and reproduction of simulation results

Akberdinir@gmail.com: /* Access to the model */

2021-05-28T11:47:14Z

‎Access to the model

Akberdinir@gmail.com: /* Simulate the model */

2021-05-28T11:46:41Z

‎Simulate the model

Akberdinir@gmail.com: /* Model availability and reproduction of simulation results */

2021-05-28T11:18:23Z

‎Model availability and reproduction of simulation results

Akberdinir@gmail.com: /* Model availability and reproduction of simulation results */

2021-05-28T11:00:39Z

‎Model availability and reproduction of simulation results

Akberdinir@gmail.com: /* Model availability and reproduction of simulation results */

2021-05-28T10:32:27Z

‎Model availability and reproduction of simulation results

← Older revision		Revision as of 08:55, 1 June 2021
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−	<p align=justify> 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 Tree area of the model project or launch the Notebook directly from GitLab using Binder web-service:</p>	+	<p align=justify> 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 Tree area of the model project (read-only mode for "demo" user) or launch the Notebook directly from GitLab using Binder web-service (registration is not required):</p>

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 |-
 |<gallery mode="packed" heights="700px">
-  Figure1_Project.png|<br><span style="font-size: 90%; align="right"">'''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.</span>
+  Figure1_Project.png|<br><span style="font-size: 90%; align="right"">'''Figure 1.''' The workspace of the model project in web-version of the BioUML platform. Two rectangles with red borders indicate the Tree area of the workspace and the corresponding place of the model project, respectively.</span>
 </gallery>
 |}
@@ Line 76: / Line 76: @@
-<p align=justify> 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:</p>
+<p align=justify> 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 Tree area of the model project or launch the Notebook directly from GitLab using Binder web-service:</p>

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 ==Model availability and reproducibility of simulation results==
 ===Access to the model===
@@ Line 58: / Line 60: @@
 </gallery>
 |}
 ===Simulate the model===

@@ Line 1: / Line 1: @@
-==Model availability and reproduction of simulation results==
+==Model availability and reproducibility of simulation results==
 ===Access to the model===
@@ Line 9: / Line 9: @@
 {| align="center" style="background:#f8f9fa; border:1px solid #c8ccd1; font-size:100%; margin-center:1em" cellspacing=0 cellpadding=0
 |-
-|<gallery mode="packed" heights="600px">
+|<gallery mode="packed" heights="700px">
   Figure1_Project.png|<br><span style="font-size: 90%; align="right"">'''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.</span>
 </gallery>
@@ Line 23: / Line 23: @@
 {| align="center" style="background:#f8f9fa; border:1px solid #c8ccd1; font-size:100%; margin-center:1em" cellspacing=0 cellpadding=0
 |-
-|<gallery mode="packed" heights="370px">
+|<gallery mode="packed" heights="700px">
    Figure2_Integrated_model.png|<br><span style="font-size: 90%; align="right"">'''Figure 2.1.''' An integrated modular model linking metabolism, Ca<sup>2+</sup>-dependent signaling transduction and regulation of gene expression in human skeletal muscle (To consider the model in more details click on the figure). </span>
    Figure2_FiberR.png|<br><span style="font-size: 90%; align="right"">'''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). </span>
 </gallery>
@@ Line 30: / Line 35: @@
 {| align="center" style="background:#f8f9fa; border:1px solid #c8ccd1; font-size:100%; margin-center:1em" cellspacing=0 cellpadding=0
 |-
-|<gallery mode="packed" heights="600px">
+|<gallery mode="packed" heights="700px">
    Figure2_CytosolR.png|<br><span style="font-size: 90%; align="right"">'''Figure 2.3.''' SBGN diagram of the cytosol compartment in fibers I type representing all metabolic reactions and corresponding math equations in the module.</span>
 </gallery>
@@ Line 43: / Line 48: @@
 {| align="center" style="background:#f8f9fa; border:1px solid #c8ccd1; font-size:100%; margin-center:1em" cellspacing=0 cellpadding=0
 |-
-|<gallery mode="packed" heights="370px">
+|<gallery mode="packed" heights="700px">
    Figure2_CytosolR_Entities.png|<br><span style="font-size: 90%; align="right"">'''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). </span>
    Figure2_CytosolR_Variables.png|<br><span style="font-size: 90%; align="right"">'''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). </span>
 </gallery>
@@ Line 56: / Line 66: @@
 {| align="center" style="background:#f8f9fa; border:1px solid #c8ccd1; font-size:100%; margin-center:1em" cellspacing=0 cellpadding=0
 |-
-|<gallery mode="packed" heights="650px">
+|<gallery mode="packed" heights="700px">
    Figure3_Simulate.png|<br><span style="font-size: 90%; align="right"">'''Figure 4.''' To run the model employ Simulation tab. </span>
 </gallery>
@@ Line 68: / Line 78: @@
 {| align="center" style="background:#f8f9fa; border:1px solid #c8ccd1; font-size:100%; margin-center:1em" cellspacing=0 cellpadding=0
 |-
-|<gallery mode="packed" heights="370px">
+|<gallery mode="packed" heights="700px">
-   Figure4_Simulate_Notebook.png|<br><span style="font-size: 90%; align="right"">'''Figure 5.1.''' An integrated modular model linking metabolism, Ca<sup>2+</sup>-dependent signaling transduction and regulation of gene expression in human skeletal muscle (To consider the model in more details click on the figure). </span>
+   Figure4_Simulate_Notebook.png|<br><span style="font-size: 90%; align="right"">'''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). </span>
-   Figure4_Simulate_Binder.png|<br><span style="font-size: 90%; align="right"">'''Figure 5.2.''' 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). </span>
+</gallery>
 </gallery>
 |}
 {| align="center" style="background:#f8f9fa; border:1px solid #c8ccd1; font-size:100%; margin-center:1em" cellspacing=0 cellpadding=0
 |-
-|<gallery mode="packed" heights="600px">
+|<gallery mode="packed" heights="700px">
-   Figure4_Simulate_Binder_opened.png|<br><span style="font-size: 90%; align="right"">'''Figure 5.3.''' SBGN diagram of the cytosol compartment in fibers I type representing all metabolic reactions and corresponding math equations in the module.</span>
+   Figure4_Simulate_Binder_opened.png|<br><span style="font-size: 90%; align="right"">'''Figure 5.3.''' Binder allows a user to launch the Notebook in an executable environment.</span>
 </gallery>
 |}

@@ Line 58: / Line 58: @@
 |<gallery mode="packed" heights="650px">
    Figure3_Simulate.png|<br><span style="font-size: 90%; align="right"">'''Figure 4.''' To run the model employ Simulation tab. </span>
 </gallery>
 |}

← Older revision		Revision as of 11:46, 28 May 2021
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	===Simulate the model===		===Simulate the model===

−	<p align=justify> There are several ways to simulate the integrated model. The first one is to select the appropriate simulation engine clicking on <b><i> Simulation Tab </i></b> which is located below the diagram and push the <b><i> Simulation button</i></b> in this engine (in the rectangle with red border):</p>	+	<p align=justify> There are several ways to simulate the integrated model. The first one is to select the appropriate simulation engine clicking on <b><i> Simulation Tab </i></b> which is located below the diagram and push the <b><i> Simulation button</i></b> in this engine (in the rectangle with a red border):</p>

@@ Line 2: / Line 2: @@
 ===Access to the model===
 <p align=justify> The modular model with all submodules as well as values of the model parameters in each module are available on <b>BioUML web-server online</b> (click [https://sirius-web.org/bioumlweb/#de=data/Collaboration%20(git)/Muscle%20metabolism/Models/Integrated%20Model%202021/ here] and use "demo" access button) or can be accessed via <b>GitLab</b> (click [https://gitlab.sirius-web.org/virtual-patient/muscle-metabolism here]). The model project is presented on the left side of the workspace:</p>
@@ Line 36: / Line 37: @@
-<p align=justify> 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 :</p>
+<p align=justify> 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:</p>
@@ Line 45: / Line 46: @@
    Figure2_CytosolR_Entities.png|<br><span style="font-size: 90%; align="right"">'''Figure 3.1.''' A Menu Tab with initial values of the model variables is highlighted by a rectangle with red border. (To consider the model in more details click on the figure). </span>
    Figure2_CytosolR_Variables.png|<br><span style="font-size: 90%; align="right"">'''Figure 3.2.''' A Menu Tab with parameter values of the model is highlighted by a rectangle with red border. (To consider the model in more details click on the figure). </span>
 </gallery>
 |}

← Older revision		Revision as of 10:32, 28 May 2021
Line 36:		Line 36:


−	<p align=justify> To consider initial values of the model variables and parameter values click on the corresponding menu tab which is located below the diagram :</p>	+	<p align=justify> 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 :</p>