tellurium v1.0.0

We are pleased to announce tellurium 1.0.0, a Python environment to model, simulate, and analyze biochemical systems using a single tool.

Tellurium "te." is a free and open source Python environment for systems and synthetic biology modeling and simulation. Our aim is to make biochemical system modeling and simulation easier, using the SBML family of standards.

You operate tellurium from the Tellurium Spyder IDE. It comes preloaded with examples using libAntimony to define models, libRoadRunner 1.1.0 (including libStruct) to simulate them, numpy and matplotlib to analyze and plot results. We also enable export to Matlab using sbml2matlab. It relies on libSBML and is extensible via tePlugins, our plugin system.

Together these packages provide a comprehensive modeling experience in Python for the novice and expert.
Experienced python developers can use tellurium outside of the Spyder IDE if they want. Seasoned users can also install other packages using the python package manager pip, e.g. StochPy, PySCeS.

Future: reproducibility using the SEDML standard

Download and install the click-through installer
http://tellurium.analogmachine.org/download/

This 1.0.0 release is for Windows. It includes example python scripts demonstrating tellurium and tePlugins use.

tePlugins examples released with this version include:
Levenberg-Marquardt
Nelder-Mead
Monte Carlo bootstrap
AddNoise
TestModel
ChiSquare

Michal Galdzicki (UW)
Totte Karlsson (DuneScientific)
Stanley Gu (UW)
Lucian Smith (UW)
Andy Somogyi (IU)
Herbert Sauro (UW)

1.0.0
bump version
changed examples to use te.plotWithLegend()

0.9.14
Safely catch errors on first import

0.9.12
RoadRunner constructor now accepts an antimony string
Start Menu Group and icons

0.9.11
Using PyQt4-4.10.3-gpl-Py2.7-Qt4.8.5-x32.exe to overcome user specific PyQt issues

0.9.10
Added config reset lines to teplugins examples

0.9.9
Updated to teplugins-1.0.13, fix for the plotting issue

0.9.5
Updated to teplugins-1.0.12
Updated to sbml2matlab_1.2.2_win32

0.9.4
Fixed teplugins version to teplugins.getVersion()
Updated to pylibroadrunner-1.1.0-win_32
Fixed issue when roadrunner dest dir did not exist, conf file was missing

0.9.3
Updated to pylibroadrunner-1.1.0-beta4-win_32.zip
Updated to TellluriumPlugins-1.0.11.zip

0.9.2
Updated to pylibroadrunner-1.1.0-beta2-win_32

0.9.1
Offline install, using pip wheels to do the install of dependencies

0.9.0
sbml2matlab now installs directly from zip distribution, using setup.py install

0.1.6
Updated to install telplugins-1.0.9
sbml2matlab export added, see te.exportToMatlab('path')

0.1.5
Updated to install pylibroadrunner-1.1.0-beta1-win_32 using python.exe setup.py install, from .zip distribution
Added roadrunner.conf conserved moiety conversion = True - set as default
Working on modifying Pip install to not use online PyPi repo, all dependencies packaged with installer, in progress

0.1.4
loadAntimonyModel now configures rr.conservedMoietyAnalysis = True

0.1.3
Added teRoadRunner(modelname) to set rr.conservedMoietyAnalysis = True

0.1.2
Removed te version number from spyder.version
Renamed startTellurium.py -> tellurium.py
Added te.readFromFile()

0.1.1
Waveform example - fixed r.selections
TelPlugins 1.0.7

0.1.0
TelPlugins 1.0.5
Plugin examples included in Documents{user}\tellurium-files

0.0.9
Opens Documents Dir: default working directory, File Open/Save is now "C:\Users{user}\tellurium-files"
Tutorial examples included
Pythonw.exe executes spyder to remove attachment to win console

0.0.8
version increment, because SourceForge did not like a file with the same name

0.0.7
Fixed run pip, now using explicit python path
Fixed to read VERSION.txt instead of VERSION
Spyder console has roadrunner, antimony, and telplugins available to the user directly
Spyder version now reflects tellurium version (static)

0.0.6
Updated to antimony-2.5.1 - statically linked libSBML
Added telplugins-1.0.0 - statically linked libSBML, removed a dev ver of a plugin
Installer updated to read PythonPath from Registry for all sub-installs
NOTICE.txt updated
Updated README.txt to include real content

0.0.5
example1.py loads by default as the opening script, just press be green 'play' button.
Python console tab is now the default active console
Option to open README.txt after install - currently blank
Option to Run Spyder after install, default option
tellurium imports as te - makes startTellurium.py commands available at te.*
getTelluriumVersion.py - displays tellurium version correctly

0.0.4
telplugins updated - import bug persists

0.0.3
NEWS.txt added - log of changes
reverted to telplugins-0127204-11.27

0.0.2
Starts tellurium automatically in spyder
Updated startTellurium.py e78c709
Added modified spyder-2.3.0dev

0.0.1
Installs the following packages:
libroadrunner-1.0.1
antimony-2.5.0
telplugins-01312014-13.02
python-2.7.6
numpy-1.8.0
matplotlib-1.3.1
PyQt4-4.10.3-gpl-Py2.7-Qt4.8.5-x32
sip.pyd
get-pip.py
spyder-2.2.5

get-pip.py
python-dateutil
pyparsing
six
ipython[all]
sphinx
pyflakes
pylint
pep8
psutil