Difference between revisions of "Systems biology - model import"

From BioUML platform
Jump to: navigation, search
 
(4 intermediate revisions by one user not shown)
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>
 
<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>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>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.
+
<li>Select the document and click on the <b>"Start"</b> button.
 +
<li>The model will appear in the BioUML repository and will be opened in a new workspace tab.
 
</ol>
 
</ol>
  
−
<h2>Adjusting model layout</h2>
+
Let's see these steps in screenshots:
  
−
[[File:systems_biology_layout.png|thumb|'''Figure 2'''. Steps to perform the model layout.]]
+
<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>
  
−
To change the default layout of the model, use <b>Layout</b> tab in the right bottom panel (Figure 2).
+
<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.
  
−
Currently, BioUML contains the folloing layout schemes:
+
<br><br>[[File:import_model_02.png]]<br><br>
−
*[[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.
+
<li>Select the document and click on the <b>"Start"</b> button.
  
−
<h2>Basic model editing</h2>
+
<br><br>[[File:import_model_03.png]]<br><br>
  
−
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).
+
<li>The model will appear in the BioUML repository and will be opened in a new workspace tab.
 +
 
 +
<br><br>[[File:import_model_04.png]]<br><br>
 +
</ol>
  
−
<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 parameters.
+
−
</gallery>
+

Latest revision as of 11:51, 16 March 2022

To import SBML model, do the following:

  1. Find the folder in the BioUML repository where you want to download the model (for example, use the temporary folder in the tree: data/Collaboration/Demo/Data/Temp). Then, right-click on this folder and select "Import".
  2. In the window that opens, click on the "Computer" button and find the document with the model in the file system of your computer.
  3. Select the document and click on the "Start" button.
  4. The model will appear in the BioUML repository and will be opened in a new workspace tab.

Let's see these steps in screenshots:

  1. Find the folder in the BioUML repository where you want to download the model (for example, use the temporary folder in the tree: data/Collaboration/Demo/Data/Temp). Then, right-click on this folder and select "Import".

    Import model 01.png

  2. In the window that opens, click on the "Computer" button and find the document with the model in the file system of your computer.

    Import model 02.png

  3. Select the document and click on the "Start" button.

    Import model 03.png

  4. The model will appear in the BioUML repository and will be opened in a new workspace tab.

    Import model 04.png

Retrieved from "https://wiki.biouml.org/index.php?title=Systems_biology_-_model_import&oldid=9689"
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox