Systems biology - manual model construction - Revision history

Akberdinir@gmail.com: /* Building from BioModels Repository */

2022-03-18T12:16:27Z

‎Building from BioModels Repository

Akberdinir@gmail.com: /* Building from BioModels Repository */

2022-03-18T12:15:17Z

‎Building from BioModels Repository

Akberdinir@gmail.com: /* Building from BioModels Repository */

2022-03-18T12:07:37Z

‎Building from BioModels Repository

Akberdinir@gmail.com at 12:07, 18 March 2022

2022-03-18T12:07:04Z

Akberdinir@gmail.com at 11:53, 18 March 2022

2022-03-18T11:53:42Z

Akberdinir@gmail.com at 11:49, 18 March 2022

2022-03-18T11:49:12Z

Akberdinir@gmail.com at 11:48, 18 March 2022

2022-03-18T11:48:46Z

Akberdinir@gmail.com: /* Building from scratch */

2022-03-18T11:20:40Z

‎Building from scratch

Akberdinir@gmail.com: /* Building from scratch */

2022-03-15T17:27:58Z

‎Building from scratch

Akberdinir@gmail.com: /* Building from scratch */

2022-03-15T17:16:12Z

‎Building from scratch

← Older revision		Revision as of 12:16, 18 March 2022
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−	To view or edit the model reaction or substance, see the section [http://wiki.biouml.org/index.php/Systems_biology_-_basic_model_editing Basic model editing] of the tutorial, while to simulate the model, look over the section dedicated to [http://wiki.biouml.org/index.php/Systems_biology_-_model_simulation Model simulation].	+	To view, edit or modify (including an extension) the model reaction or substance, see the section [http://wiki.biouml.org/index.php/Systems_biology_-_basic_model_editing Basic model editing] of the tutorial, while to simulate the model, look over the section dedicated to [http://wiki.biouml.org/index.php/Systems_biology_-_model_simulation Model simulation].

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 ==Building from BioModels Repository==
 <font size="3">
-To analyze developed and published model or use this one as a basis for modification/extension, you can employ [https://www.ebi.ac.uk/biomodels/ BioModels] repository the folder of that is represented under <b><i>Databases</i></b> tab in the <b>Tree Area</b>. Select the Biomodels repository by a single click with the left mouse button, then double-click will open the subdirectory (Diagrams→Curated).
+To analyze developed and published model or use this one as a basis for modification/extension, you can employ [https://www.ebi.ac.uk/biomodels/ BioModels] repository the folder of that is represented under <b><i>Databases</i></b> tab in the <b>Tree Area</b> (marked red below). Select the Biomodels repository by a single click with the left mouse button, then double-click will open the subdirectory (Diagrams→Curated).
@@ Line 41: / Line 41: @@
-To open model of interests, double-click of the left mouse button the model icon in the  <b>Tree Area</b> or a single-click of the right mouse button on the icon and press  <b><i>Open</i></b> in a pop-up window.
+To open model of interests, double-click of the left mouse button the model icon in the  <b>Tree Area</b> or a single-click of the right mouse button on the icon and press  <b><i>Open</i></b> in a pop-up window (marked red below).
@@ Line 49: / Line 49: @@
-The model diagram (for instance, [https://ict.biouml.org/bioumlweb/#de=databases/Biomodels/Diagrams/Curated/BIOMD0000000211 BIOMD0000000211, Albert2005_Glycolysis]) will be opened in the <b>Work Space</b>, while the model equations and values of the model parameters/variables will be appeared in the <b><i>Model</i></b> tab of the <b>Operations Field</b> (see [http://wiki.biouml.org/index.php/Systems_biology_-_Get_started Get started]).
+The model diagram (for instance, [https://ict.biouml.org/bioumlweb/#de=databases/Biomodels/Diagrams/Curated/BIOMD0000000211 BIOMD0000000211, Albert2005_Glycolysis]) will be opened in the <b>Work Space</b>, while the model equations and values of the model parameters/variables will be appeared in the <b><i>Model</i></b> tab (marked red below) of the <b>Operations Field</b> (see [http://wiki.biouml.org/index.php/Systems_biology_-_Get_started Get started]).

@@ Line 36: / Line 36: @@
-[[File:Bulding_BioModels_Fig1.png|1000px]]
+[[File:Building_BioModels_Fig1.png|1000px]]
 <span style="font-size: 90%"> '''Figure 1.''' BioModelsDB repository in corresponding tab of the <b>Tree Area</b>.</span>
@@ Line 44: / Line 44: @@
-[[File:Bulding_BioModels_Fig2.png|1000px]]
+[[File:Building_BioModels_Fig2.png|1000px]]
 <span style="font-size: 90%"> '''Figure 2.''' Opening previously developed model from BioModelsDB in BioUML.</span>
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-[[File:Bulding_BioModels_Fig3.png|1000px]]
+[[File:Building_BioModels_Fig3.png|1000px]]
 <span style="font-size: 90%"> '''Figure 3.''' The <b><i>Model</i></b> tab contains subtabs with details about model entities, variables, equations etc.</span>

← Older revision		Revision as of 12:07, 18 March 2022
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	The model diagram (for instance, [https://ict.biouml.org/bioumlweb/#de=databases/Biomodels/Diagrams/Curated/BIOMD0000000211 BIOMD0000000211, Albert2005_Glycolysis]) will be opened in the <b>Work Space</b>, while the model equations and values of the model parameters/variables will be appeared in the <b><i>Model</i></b> tab of the <b>Operations Field</b> (see [http://wiki.biouml.org/index.php/Systems_biology_-_Get_started Get started]).		The model diagram (for instance, [https://ict.biouml.org/bioumlweb/#de=databases/Biomodels/Diagrams/Curated/BIOMD0000000211 BIOMD0000000211, Albert2005_Glycolysis]) will be opened in the <b>Work Space</b>, while the model equations and values of the model parameters/variables will be appeared in the <b><i>Model</i></b> tab of the <b>Operations Field</b> (see [http://wiki.biouml.org/index.php/Systems_biology_-_Get_started Get started]).
		+
		+
		+	[[File:Bulding_BioModels_Fig3.png\|1000px]]
		+
		+	<span style="font-size: 90%"> '''Figure 3.''' The <b><i>Model</i></b> tab contains subtabs with details about model entities, variables, equations etc.</span>
		+
		+
		+	To view or edit the model reaction or substance, see the section [http://wiki.biouml.org/index.php/Systems_biology_-_basic_model_editing Basic model editing] of the tutorial, while to simulate the model, look over the section dedicated to [http://wiki.biouml.org/index.php/Systems_biology_-_model_simulation Model simulation].

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 A pathway diagram opened in the work space has a tool bar as shown below:
 <br><br>[[File:Model_fromscratch_Fig4.png]]<br><br>
-</font size="3">
 <h5>Adding a new element to the diagram</h5>
 ==Building from BioModels Repository==
@@ Line 43: / Line 47: @@
 <span style="font-size: 90%"> '''Figure 2.''' Opening previously developed model from BioModelsDB in BioUML.</span>

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 ==Building from scratch==
 <font size="3">
 The model development process is initiated by creation of the model network or {{Type link|diagram}}. A new diagram can be made in the <b>Work Space</b> by two methods:
 <ol>

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 Upon selecting the type of a diagram and clicking <i>Ok</i> button a new node <b><i>New Diagram</i></b> will appear in the <b>Tree Area</b> and the corresponding tab is opened in the <b>Work Space</b> to start the diagram creation.
-<br><br>[[File:Model_fromscratch_Fig3_1.png]]<br><br>
+<br><br>[[File:Model_fromscratch_Fig3_1_18_03.png]]<br><br>
 A pathway diagram opened in the work space has a tool bar as shown below:

@@ Line 3: / Line 3: @@
 <h3><b>Creation of a new diagram</b></h3>
 <font size="3">
-The model development process is initiated by creation of the model network or diagram. A new diagram can be made in the <b>Work Space</b> by two methods:
+The model development process is initiated by creation of the model network or {{Type link|diagram}}. A new diagram can be made in the <b>Work Space</b> by two methods:
 <ol>
 <li>via <b>Control Panel → New Diagram</b> (<b>Note</b>: please select the correct folder for a new diagram in your project area):
@@ Line 14: / Line 14: @@
 </ol>
-The platform will ask you to select the diagram type and specify the diagram name you want to create in the work space. In the following, the creation of a new <b><i>“SBML model in SBGN notation”</i></b> will be described.
+The platform will ask you to select the {{Type link|diagram}} type and specify the {{Type link|diagram}} name you want to create in the work space. In the following, the creation of a new <b><i>“SBML model in SBGN notation”</i></b> will be described.
 <br><br>[[File:Model_fromscratch_Fig3.png]]<br><br>