Announce: new versions of Tellurium, Roadrunner, and Antimony

[Lucian Smith]

The Sauro lab is happy to announce new versions of three of our software packages:

* Tellurium v2.2.9

* Roadrunner v2.5.0

* Antimony v2.14

Tellurium is our python 'front end' for several packages, with Antimony being our human-readable model definition language that translates to SBML, and Roadrunner being our robust and fast SBML simulator.  While all three are available from Python, both Roadrunner and Antimony are available as C/C++ libraries that may be used in other contexts and even in other software packages (you could use Antimony as a way to allow your own software's users to input SBML models, for example.)

Highlights of these releases include:
* No more 'ncurses' dependency for roadrunner
* Algebraic rules can now be encoded in Antimony (though they are not simulatable in Roadrunner)
* Named stoichiometries can be encoded in Antimony
* Stoichiometries can now be set in Tellurium with 'setValue', whether or not they were named.
* Improved SED-ML support in Tellurium.
* More annotations can now be encoded in Antimony, as can 'notes'.
* Fix handling of some reactions in the gillespie integrator
* Allow setting init(x) when x had an initial assignment in Roadrunner/Tellurium.
* getCurrentSBML no longer exports initial assignments that no longer apply in Roadrunner/Tellurium.
* getValue('time') now returns the actual current time in Roadrunner/Tellurium
* The steady state selection vector now doesn't change once set in Roadrunner/Tellurium
* New 'fluxThreshold' setting for when to zero out flux control coefficients in Roadrunner/Tellurium

Python bindings for all three packages are available for from pypi, using the package names:

* tellurium

* libroadrunner

* antimony

Binaries and source code can also be downloaded from github:

https://github.com/sys-bio/tellurium/releases

https://github.com/sys-bio/roadrunner/releases

https://github.com/sys-bio/antimony/releases/

All comments, including bug reports and feature requests, are welcome!  

-Lucian Smith