Outline

 

Overview

SBML importer Plugin for PathVisio allow researchers to visualize and overlay data on the same pathway models which they use in simulation experiments.The plugin facilitates model curation and extension by providing modelers with an up-to-date graphical (SBGN-PD) representation of their model.

The plugin also enables:

  • SBML model validation.
  • Direct import of SBML models from Biomodels database.
  • Visualization of SBML elements.
  • Bio model search by Bio model name, Publication name/id, Person name, Taxonomy id, Uniprot id, CHEBI Id and GO Id.
  • Applying layout to the imported SBML model.
  • Visualization of the annotations of an SBML model.
  • SBML model export.

validation

 

Figure 1: This shows the validate button.

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Figure 2: This shows the on click event of validate button. The dialog box contains two buttons, one to browse the file from the system and the other to validate the selected file.

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Figure 3: Selecting an SBML file to validate.

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Figure 4: After clicking on the Validate the file button, the results are shown in the output panel.

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Figure 5: This shows the Biomodels button.

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Figure 6: Type the search term in the appropriate search box and click on search.

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Figure 7: The search results are displayed.

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Figure 8: Clicking on the search result will import the model into the pathvisio editor.

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Figure 9: Visualization of the elements of the imported bio model in the form of tree view.

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Figure 10: Visualization of the annotations of the selected data nodes of the imported model.

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Figure 11: This shows an imported bio model before applying the layout.

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Figure 12: After clicking on the force directed layout button, the elements of the bio model are re arranged.

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Figure 13: This picture shows the export button under the File menu of the Pathvisio editor.

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Figure 14: Choose a file name and select the file type as SBML from the drop down.[After clicking on the Export button.]

 

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Figure 15: The output of the exported file.

Installation Instructions:

The PathSBML plugin depends on the SBGN plugin. Hence, first you need to install SBGN plugin.

Install SBGN Plugin:

  1. Go to Plugins → Plugin Manager
  2. Select SBGN plugin from the list of available plugins and install it.

Install PathSBML Plugin:

You can install the plugin locally by following the following steps:

  1. Download the zip file containing the PathSBML.jar
  2. Download and start PathVisio by clicking pathvisio.jnlp
  3. Go to Plugins → Install local plugin
  4. Browse -> Choose the folder where the downloaded jar file is
  5. Click Start
  6. Select the checkbox next to SBML.jar
  7. Click OK
  8. The plugin manager should give a message that the plugin is now installed
  9. You can see that the SBML side pane and the validation,forcedirectedlayout,biomodels buttons appear.

You can also compile the source code from the online repository directly.(https://github.com/applecool/SBML-importer-plugin)