Systems biology - model import - Revision history

Elena.kutumova@biouml.org at 04:51, 16 March 2022

2022-03-16T04:51:53Z

Elena.kutumova@biouml.org at 04:44, 16 March 2022

2022-03-16T04:44:35Z

Elena.kutumova@biouml.org at 04:41, 16 March 2022

2022-03-16T04:41:40Z

Elena.kutumova@biouml.org at 03:45, 11 March 2022

2022-03-11T03:45:16Z

Elena.kutumova@biouml.org at 03:36, 11 March 2022

2022-03-11T03:36:32Z

Elena.kutumova@biouml.org at 03:33, 11 March 2022

2022-03-11T03:33:23Z

Elena.kutumova@biouml.org at 03:19, 11 March 2022

2022-03-11T03:19:29Z

Elena.kutumova@biouml.org at 02:48, 11 March 2022

2022-03-11T02:48:13Z

Elena.kutumova@biouml.org at 02:31, 11 March 2022

2022-03-11T02:31:30Z

Elena.kutumova@biouml.org at 06:26, 10 March 2022

2022-03-10T06:26:00Z

@@ Line 3: / Line 3: @@
 <ol>
 <li>Find the folder in the BioUML repository where you want to download the model (for example, use the temporary folder in the tree: <i>data/Collaboration/Demo/Data/Temp</i>). Then, right-click on this folder and select <b>"Import"</b>.
 <br><br>[[File:import_model_01.png]]<br><br>

@@ Line 18: / Line 18: @@
 <br><br>[[File:import_model_04.png]]<br><br>
 </ol>
 </font>

@@ Line 1: / Line 1: @@
-[[File:systems_biology_import.png|thumb|'''Figure 1'''. Steps to import a model.]]
+<font size="3">
 To import SBML model, do the following:
-To import SBML model, do the following (Figure 1):
 <ol>
 <li>Find the folder in the BioUML repository where you want to download the model (for example, use the temporary folder in the tree: <i>data/Collaboration/Demo/Data/Temp</i>). Then, right-click on this folder and select <b>"Import"</b>.
 <li>In the window that opens, click on the <b>"Computer"</b> button and find the document with the model in the file system of your computer.
-<li>Select this document and click on the <b>"Start"</b> button. After that, the model will appear in the BioUML repository and will be opened in a new workspace tab.
 </ol>
 <h2>Adjusting model layout</h2>
-[[File:systems_biology_layout.png|thumb|'''Figure 2'''. Steps to perform the model layout.]]
+To change the default layout of the model, use the <b>Layout</b> tab in the right bottom panel.
-To change the default layout of the model, use the <b>Layout</b> tab in the right bottom panel (Figure 2).
+<br>[[File:model_layout_01.png]]<br><br>
 Currently, BioUML contains the folloing layout schemes:
@@ Line 21: / Line 32: @@
 *[[Grid layout]]
-Select the desired scheme and click on the <b>Prepare layout</b> button [[File:Execute_icon.png]]. The newly generated layout will be shown on the right in the same tab. Then, click on the <b>Apply layout</b> button [[File:Add2docpane_icon.png]] to apply this layout to the model diagram in the document pane.
+<br>Select the desired scheme and click on the <b>Prepare layout</b> button [[File:Execute_icon.png]]. The newly generated layout will be shown on the right in the same tab.
 <h2>Basic model editing</h2>
-To edit any entity or reaction of the model, click on the corresponding element in the diagram and then click the <b>Edit</b> button [[File:Edit_icon.png]] (Figures 3-4). To edit model variables, use the <b>Variables</b> tab and after making changes, click the <b>Save</b> button [[File:Save_icon.png]] to reflect these changes in the current version of the model.
+To edit any entity of the model, click on the corresponding element in the diagram and then click the <b>Edit</b> button [[File:Edit_icon.png]].
-<gallery>
+</font>
-File:systems_biology_egiting_entities.png|'''Figure 3'''. Egiting entities.
-File:systems_biology_egiting_reactions.png|'''Figure 4'''. Egiting reactions.
-File:systems_biology_egiting_parameters.png|'''Figure 5'''. Egiting variables.
-</gallery>

@@ Line 25: / Line 25: @@
 <h2>Basic model editing</h2>
-To edit any entity or reaction of the model, click on the corresponding element in the diagram and then click the <b>Edit</b> button [[File:Edit_icon.png]] (Figures 3-4). To edit model variables, use the <b>Variables</b> tab.
+To edit any entity or reaction of the model, click on the corresponding element in the diagram and then click the <b>Edit</b> button [[File:Edit_icon.png]] (Figures 3-4). To edit model variables, use the <b>Variables</b> tab and after making changes, click the <b>Save</b> button [[File:Save_icon.png]] to reflect these changes in the current version of the model.
 <gallery>

@@ Line 12: / Line 12: @@
 [[File:systems_biology_layout.png|thumb|'''Figure 2'''. Steps to perform the model layout.]]
-To change the default layout of the model, use <b>Layout</b> tab in the right bottom panel (Figure 2).
+To change the default layout of the model, use the <b>Layout</b> tab in the right bottom panel (Figure 2).
 Currently, BioUML contains the folloing layout schemes:
@@ Line 25: / Line 25: @@
 <h2>Basic model editing</h2>
-To edit any entity or reaction of the model, click on the corresponding element in the diagram and then click the <b>Edit</b> button [[File:Edit_icon.png]] (Figures 3-4).
+To edit any entity or reaction of the model, click on the corresponding element in the diagram and then click the <b>Edit</b> button [[File:Edit_icon.png]] (Figures 3-4). To edit model variables, use the <b>Variables</b> tab.
 <gallery>
 File:systems_biology_egiting_entities.png|'''Figure 3'''. Egiting entities.
 File:systems_biology_egiting_reactions.png|'''Figure 4'''. Egiting reactions.
-File:systems_biology_egiting_parameters.png|'''Figure 5'''. Egiting parameters.
+File:systems_biology_egiting_parameters.png|'''Figure 5'''. Egiting variables.
 </gallery>

← Older revision		Revision as of 03:19, 11 March 2022
Line 22:		Line 22:

	Select the desired scheme and click on the <b>Prepare layout</b> button [[File:Execute_icon.png]]. The newly generated layout will be shown on the right in the same tab. Then, click on the <b>Apply layout</b> button [[File:Add2docpane_icon.png]] to apply this layout to the model diagram in the document pane.		Select the desired scheme and click on the <b>Prepare layout</b> button [[File:Execute_icon.png]]. The newly generated layout will be shown on the right in the same tab. Then, click on the <b>Apply layout</b> button [[File:Add2docpane_icon.png]] to apply this layout to the model diagram in the document pane.
		+
		+	<h2>Basic model editing</h2>
		+
		+	To edit any visual element on the diagram, click on it.
		+
		+	<gallery>
		+	File:systems_biology_egiting_entities.png\|Egiting entities
		+	File:systems_biology_egiting_reactions.png\|Egiting reactions
		+	File:systems_biology_egiting_parameters.png\|Egiting parameters
		+	</gallery>

← Older revision		Revision as of 02:48, 11 March 2022
Line 10:		Line 10:
	<h2>Adjusting model layout</h2>		<h2>Adjusting model layout</h2>

−	[[File:systems_biology_layout.png\|thumb\|Steps to perform the model layout.]]	+	[[File:systems_biology_layout.png\|thumb\|Figure 2. Steps to perform the model layout.]]
		+
		+	To change the default layout of the model, use <b>Layout</b> tab in the right bottom panel (Figure 2).
		+
		+	Currently, BioUML contains the folloing layout schemes:
		+	*[[Hierarchical layout]] (default)
		+	*[[Orthogonal layout]]
		+	*[[Force directed layout]]
		+	*[[Cross cost grid layout]]
		+	*[[Grid layout]]
		+
		+	Select the desired scheme and click on the <b>Prepare layout</b> button [[File:Execute_icon.png]]. The newly generated layout will be shown on the right in the same tab. Then, click on the <b>Apply layout</b> button [[File:Add2docpane_icon.png]] to apply this layout to the model diagram in the document pane.

← Older revision		Revision as of 02:31, 11 March 2022
Line 1:		Line 1:
		+	[[File:systems_biology_import.png\|thumb\|Figure 1. Steps to import a model.]]

−	~~[[File~~:~~systems_biology_import.png\|thumb\|Steps~~ to ~~import a~~ model.]]	+	To import SBML model, do the following (Figure 1):
		+	<ol>
		+	<li>Find the folder in the BioUML repository where you want to download the model (for example, use the temporary folder in the tree: <i>data/Collaboration/Demo/Data/Temp</i>). Then, right-click on this folder and select <b>"Import"</b>.
		+	<li>In the window that opens, click on the <b>"Computer"</b> button and find the document with the model in the file system of your computer.
		+	<li>Select this document and click on the <b>"Start"</b> button. After that, the model will appear in the BioUML repository and will be opened in a new workspace tab.
		+	</ol>
		+
		+	<h2>Adjusting model layout</h2>

	[[File:systems_biology_layout.png\|thumb\|Steps to perform the model layout.]]		[[File:systems_biology_layout.png\|thumb\|Steps to perform the model layout.]]

← Older revision		Revision as of 06:26, 10 March 2022
Line 1:		Line 1:

−	[[File:systems_biology_import.png\|thumb\|Steps to import a model]]	+	[[File:systems_biology_import.png\|thumb\|Steps to import a model.]]
		+
		+	[[File:systems_biology_layout.png\|thumb\|Steps to perform the model layout.]]