Difference between revisions of "Systems biology - manual model construction"
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A pathway diagram opened in the work space has a tool bar as shown below: | A pathway diagram opened in the work space has a tool bar as shown below: | ||
<br><br>[[File:Model_fromscratch_Fig4.png]]<br><br> | <br><br>[[File:Model_fromscratch_Fig4.png]]<br><br> | ||
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<h5>Adding a new element to the diagram</h5> | <h5>Adding a new element to the diagram</h5> | ||
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==Building from BioModels Repository== | ==Building from BioModels Repository== | ||
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<span style="font-size: 90%"> '''Figure 2.''' Opening previously developed model from BioModelsDB in BioUML.</span> | <span style="font-size: 90%"> '''Figure 2.''' Opening previously developed model from BioModelsDB in BioUML.</span> | ||
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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]). | ||
Revision as of 18:53, 18 March 2022
Contents |
Building from scratch
Creation of a new diagram
The model development process is initiated by creation of the model network or 
diagram. A new diagram can be made in the Work Space by two methods:
- via Control Panel → New Diagram (Note: please select the correct folder for a new diagram in your project area):
- via the Tree Area by a single click with the right mouse button on the corresponding folder of the project:
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 “SBML model in SBGN notation” will be described.
Upon selecting the type of a diagram and clicking Ok button a new node New Diagram will appear in the Tree Area and the corresponding tab is opened in the Work Space to start the diagram creation.
A pathway diagram opened in the work space has a tool bar as shown below:
Adding a new element to the diagram
Building from BioModels Repository
To analyze developed and published model or use this one as a basis for modification/extension, you can employ BioModels repository the folder of that is represented under Databases tab in the Tree Area. Select the Biomodels repository by a single click with the left mouse button, then double-click will open the subdirectory (Diagrams→Curated).
Figure 1. BioModelsDB repository in corresponding tab of the Tree Area.
To open model of interests, double-click of the left mouse button the model icon in the Tree Area or a single-click of the right mouse button on the icon and press Open in a pop-up window.
Figure 2. Opening previously developed model from BioModelsDB in BioUML.
The model diagram (for instance, BIOMD0000000211, Albert2005_Glycolysis) will be opened in the Work Space, while the model equations and values of the model parameters/variables will be appeared in the Model tab of the Operations Field (see Get started).
