No description, website, or topics provided.
Java
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
META-INF
bin/org/pathvisio/sbml
build
dist
lib
src/org/pathvisio/sbml
test/org/pathvisio/sbml
testdata
README.md
build.properties
build.xml

README.md

SBML-importer-plugin

SBML importer Plugin for PathVisio allow researchers to visualize and overlay data on the same pathway models which they use in simulation experiments. It provides a better visualization of the models and layouts in SBML and an export feature which enables the user to export the models and layouts in SBML format.

Currently the development of the plugin is in progress.Right now, the plugin does the following:

  • Importing an SBML file into the pathvisio editor.
  • Viewing the elements of an imported SBML model.
  • Biomodel integration - importing the models directly from the bio model database
  • Visualization of the annotations of an imported SBML model.
  • Applying the layout to the imported SBML model.
  • Validation of the SBML models.
  • Exporting the SBML model - round conversion [GPML->SBML]

The jar file of the SBML plugin can be downloaded from the following link: https://app.box.com/s/d39lkuowd2woub3cac4r

Note: SBML plugin depends on SBGN. Hence while installing the plugin in the Pathvisio Editor from the local machine through the plugin manager, first install the SBGN plugin (Plugins -> Plugin Manager)and then install the SBML plugin following the steps below:

  • Download the jar file using the link provided above
  • Click on Plugins -> Install local plugins
  • Browse -> Choose the folder where the downloaded jar file is
  • Click Start
  • Select the checkbox next to SBML.jar
  • Click OK

Refer: http://plugins.pathvisio.org/sbml2gpml/blog/

Tutorials: http://plugins.pathvisio.org/sbml2gpml/tutorials/

Contact: Anwesha Bohler: pennatula@gmail.com Sri Harsha : kmitharsha@gmail.com