Copyright 2014-2016 Kiri Choi, Matthias König, J Kyle Medley, Kaylene Stocking, Caroline Cannistra, Michal Galdzicki, and Herbert Sauro
Parmeter scan example courtesy of Matthias König
Tellurium is a python environment based on the Spyder2 IDE for building, simulating, and analysing models of biochemical networks, including gene regulatory networks, metabolic networks, and signaling pathways. It combines state-of-the-art scientific Python libraries, such as NumPy and SciPy, and includes special-purpose systems biology Python tools. Out of the box, Tellurium includes libRoadRunner, Antimony, PhraSED-ML, libSBML (via its Python bindings), and libSED-ML.
The Tellurium project is funded from the NIH/NIGMS (GM081070).
import tellurium as te
rr = te.loada('''
model example0
S1 -> S2; k1*S1
S1 = 10
S2 = 0
k1 = 0.1
end
''')
result = rr.simulate(0, 40, 500)
te.plotArray(result)
http://tellurium.readthedocs.org/en/latest/
The source code for the Tellurium Python package is hosted at https://github.com/sys-bio/tellurium and is licensed under the Apache License, Version 2.0. Tellurium uses third-party dependencies which may be licensed under different terms. Consult the documentation for the respective third-party packages for more details.
TELLURIUM AND ALL SOFTWARE BUNDLED WITH TELLURIUM (HEREAFTER "THE SOFTWARE") IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THE SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.