Spyder Plugins

Network viewer

The network viewer allows a user to display an SBML model as a network. If a model has no layout information the network viewer will create a layout based on a force-spring algorithm. If the SBML does contain a layout the viewer will use that.

The viewer can be used either from the console or from the viewer graphical user interface.

To view an Antimony model use the code:

import nwed
import tellurium as te

model = '''
S1 -> S2; v; 
S2 -> S3; v;
'''
nwed.setsbml (te.antimonyToSBML (model))

To view a SBML model from a file use the code:

import nwed
import tellurium as te

nwed.setsbml (te.readFromFile ('mymodel.xml'))

To get the SBML from the viewer use the following code:

import nwed
sbmlStr = nwed.getsbml ()

The plugin also provides a library to manipulate the SBML layout extension, i.e. add layout to SBML model that has none. Further details can be found at:
libSBNW documentation and the hosting Github page

Import plugins

Tellurium allows simple GUI based plugins for importing COMBINE and SED-ML files. For more information on COMBINE and SED-ML support in Tellurium, see SEDML Support page.

To use the plugin, open File menu and go to Import. Here, you have the option to import either a COMBINE Archive or SED-ML files in Python script or PhraSED-ML script.

filemenu

A window to select the file to translate will pop up:

selectscreen

Choose a file to translate, and press Open. Translated files will be opened in a new editor window. Save the file and now you can directly run the code using the console. Any SBML files described in the manifest file of COMBINE archive will be translated into Antimony by default.

output

Rate Law Template

The Rate Law Templates plugin provides a dictionary of commonly used rate equations in systems biology. The plugin allows users to insert equations to the editor window (optionally renaming the equation parameters to match the user’s own variable names). Currently, the library consists of 47 different rate laws which can be easily expanded through updating the rate law database.

If you do not see a tab for either the network viewer or the rate law template, go to View -> Panes and make sure Network viewer and RateLaw are checked