News

October 2017, Release 2.0.3

This is the first stable release to feature 64-bit Python and Spyder 3.0+ as default for Tellurium IDE. There has been major updates to COMBINE support.

IDE Updates:

September 2017, Release 2.0.0 (Beta)

This is the first release to feature the Tellurium notebook and use libCombine for reading/writing COMBINE archives.

  • Updated Roadrunner to 1.4.18.
  • Updated tellurium.py to 2.0.0.
  • Add an API to Tellurium for reading/writing COMBINE archives.
  • Include libcombine 0.2.0 (version numbers may differ).

General news:

  • In an effort to consolidate all of Tellurium’s documentation, we have migrated all of the documentation on this site to readthedocs.org. Please find Tellurium’s documentation here.

February 2017, Release 1.3.6 (IDE only)

Download Windows Installer here

September 2016, Release 1.3.5 (IDE only)

Download Windows Installer here
Download the Mac version here

  • Included pysbol2
  • Updated tellurium.py to 1.3.5
  • Due to upstream issues, the Mac version of the IDE has been deprecated in favor of the Tellurium notebook front-end

August 2016, Release 1.3.4

Download Windows Installer here
Download the Mac version here

  • Updated Roadrunner to 1.4.8
  • Updated tellurium.py to 1.3.4
  • Minor updates on tecombine module
  • Fixed issues with the COMBINE archive export
  • Minor bug fixes

May 2016, Release 1.3.3

Download Windows Installer here
Download the Mac version here

  • Updated Roadrunner to 1.4.5
  • Updated tellurium.py to 1.3.3
  • Updated phraSED-ML to 1.0.3
  • Updated SEDML translation
  • Updated COMBINE support
  • Updated pip, Jinja2

March 2016, Release 1.3.2

Download Windows Installer here
Download the Mac version here

January 2016, Release 1.3.0

Download Windows Installer here
Download the Mac version here

October 2015, Release 1.2.4

Download Windows Installer here
Download the Mac version here

  • Updated Roadrunner to 1.4.0
  • Updated Antimony to 2.8.0
  • Updated PhrasedML to 0.5beta
  • Using –reset and –default arguments for Spyder will function properly
  • New plugins: import SEDML/combine as PhrasedML
  • Updated SED-ML conversion
  • Updated import combine, import SEDML, and openSBML plugins
  • Updated simpleSBML
  • New feature: Export to Combine
  • Updated example files

August 2015, Release 1.2.3

Download Windows Installer here
Download the Mac version here

  • Updated Winpython to 2.7.10.1 (Python 2.7.10, Spyder 2.3.5.2, PyQt 4.11.4, IPython 3.2.0 and more)
  • Fixed stochiometry issue in simplesbml
  • Updated tePlugins to 1.1.1
  • New Plugin: openSBML
  • New Package: phrasedML, matplotlib2tikz
  • Updated SED-ML conversion
  • Updated installer
  • Updated Tellurium examples

June 2015, Release 1.2.2

Download Windows Installer here
Download the Mac version here

May 2015, Release 1.2.1

Download Windows Installer here
Download the Mac version here

  • New package added: simpleSBML, jsonschema
  • Improved translation from SED-ML to python
  • Improved Import Plugins
  • Updated sbnw to 1.3.2
  • Changed default location of Tellurium docs

April 2015, Release 1.2.0

Note that we install a completely separate python system so that your existing python setup will not be changed.

Download Windows Installer here
Download the Mac version here

  • Updated Winpython to 2.7.9.4 (Spyder 2.3.4, numpy 1.9.2, matplotlib 1.4.3, scipy 0.15.1, and more)
  • Incorporated pySBOL
  • Updated libRoadRunner to 1.3.2
  • Updated libSBML to 5.11.4
  • Updated sbnw
  • Improved installer UI and installation time
  • Minor UI improvements
  • Fixed text files

March 2015, Release 1.1.8

  • Now previous settings are carried over to newer installation
  • New package added: control 0.6d
  • Updated libRoadRunner to 1.3.1
  • Updated Antimony to 2.7.0
  • Updated sbnw
  • New templates in Spyder will automatically import tellurium and roadrunner
  • Minor bug fixes

January 2015, Release 1.1.7

Download Windows Installer here.
Download the Mac version here. Any issues contact Andy Somogyi

Changes to Tellurium 1.1.6 to 1.1.7

  • Updated Tellurium installer using latest WinPython
  • Updated libRoadRunner to 1.3.0
  • Updated libAntimony to 2.6
  • Improved sedml/archive import
  • New network visualization plugin by Kyle Medley
  • Fixed two minor bugs in the tellurium library (plotting and reaction rates)
  • Fixed some errors in the documentation pages
  • Updates to documentation (eg libroadrunner).

September 2014, Release 1.1.6

Download Windows Installer here. For the Mac version contact Andy Somogyi

Changes to Tellurium 1.1.5 to 1.1.6

  • New completely self-contained Tellurium installer using WinPython
  • Added new spyder plugins. – Sedml2py, Combine2py
  • Added libSBML 5.10.0 Python bindings
  • Updated to IPython 2.0.0
  • Updated to Numpy 1.8.1
  • Minor changes in Spyder config.py

Changes to libRoadRunner (Andy Somogyi)

Version 1.2.6

  • Python dynamic properties are now on the RoadRunner instead of the RoadRunner.model object
  • Fixed bug in dynamic properties where they were not cleared when a new model is loaded.
  • Added boundary species to python dynamics properties
  • Redesign dynamic property generations – new code is much cleaner.
  • Testing files in roadrunner.testing are automatically enumerated and run from roadrunner.testing.test_files
  • Fix for ordering variables correctly when creating an SimulateOptions from a libSBML test suite txt file.
  • If model has comp extension, automatically flatten.
  • Note, libSBML comp extension has numerous memory issues, comp extension models *might* cause instability.
  • Upgrade to libSBML 5.10.2
  • All logging output is re-directed to the IPython socket when running in the QT IPython console. This allows allows logging messages to show up in the IPython console.
  • Support mixed mode arithmetic. workarounds for buggy MSVC stdlib functions.
  • Significantly improve error messages for mal-formed SBML models.

July 20 2014, Release 1.1.5

Download Windows Installer here.

Changes from 1.1.4 to 1.1.5

  • Update to latest libRoadRunner 1.2.5
  • Updated to use modified version of Spyder 2.3.0
  • Installs (but does not yet use) libSEDML 0.3.0
  •  All Tellurium methods now documented in new Docs on Tell web site
  • Additional methods available:
    New examples and model sincluded with distribution
    Added Jarnac compatiblity methods
    Added getMatlab and getAntimony methods
    Added listOfModels(), loadTestModel(), getTestModel
    Added reset, resetAll and resetToOrigin methods
    Added loada shortcut to loadAntimonyModel

New Mac full installer available from Andy Somogyi.

July 20 2014, Release 1.1.4

Download Windows Installer here.

Changes from 1.1.3 to 1.1.4

  • Update to getRatesOfChange, returns full dy/ddt when there are conserved moieties
  • Added exportToMatlab and getMatlab, eg

r = roadrunner.RoadRunner (‘mymodel.xml’)
print r.getMatlab()

  • Added more Jarnac compatibility routines
  • Improved plotting routines from roadrunner
  • New documentation page for all Tellurium methods and examples

July 20 2014, Release 1.1.3

Download Windows Installer here.

Changes from 1.1.1 to 1.1.3

  • Added new methods to help users more easily carry out Gillespie simulations
  • Better error messages from Antimony when there are errors
  • Added setSeed(), getSeed() and Gillespie to a roadrunner instance.
  • Added getRatesOfChange() method to roadrunner instance to match names of related methods (Makes it easier to find using intellisense).
  • Added noticesOn and noticiesOff to make it easier to suppress notices from roadRunner.

Example Gillespie simulation (Note that Gillespie can now be called directly from the roadrunner instance):

import tellurium as te

model = '''
S1 -> S2; k1*S1;
S2 -> S1; k2*S2;

k1 = 0.2; k2 = 0.1;
S1 = 40; S2 = 0
'''

r = te.loadAntimonyModel (model)
r.setSeed (1234)
for i in range(1,10):
    result = r.gillespie(0, 50)
    te.plotArray (result)
    r.reset()

Updated to use libRoadRunner 1.2.3.

Changes from 1.1.0 to 1.1.1

Update to use libRoadRunner 1.2.1.

Added a  new method to the tellurium startup file to make it easy to run a stochastic simulation from roadRunner:

result = te.gillespie (roadrunerInstance, startTime, EndTime, [stepsize])

Without the step size gillespie will use the normal variable step size algorithm., With the step size output will be on a grid determined by the step size.

For example:

import roadrunner
import tellurium

ant = ”’
model cell()
A -> B; k1*A;

A = 60; k1 = 0.001;
end;
”’

r = te.loadAntimonyModel (ant)
result = te.gillespie (r, 0, 6000)
te.plotWithLegend (r, result)

May 12 2014, Release 1.1.0

Download binaries here.

Changes from 1.0.0 to 1.1.0

Update to use libRoadRunner 1.2.0

Added a range of new methods to the tellurium startup file:

def loadSBMLModel (sbml)
def loadCellMLModel (cellML)
def antimonyTosbml (antStr)
def sbmlToAntimony (str)
def cellmlFileToAntimony (CellMLFileName)
def cellmlFileToSBML (CellMLFileName)
def cellmlStrToAntimony (CellMLStr)
def cellmlStrToSBML (CellMLStr)
def getEigenvalues (m)
def exportToMatlab (r, filename)

For example to export a loaded SBML model use the call:

te.exportToMatlab (r, “c:\myfile.m”)

where r is a roadrunner instance.