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We are* pleased to announce the release of Antimony v2.0 and 2.1-beta at

http://antimony.sourceforge.net/

where you can get windows binaries, source code, and documentation.

=================
What has changed?
=================

In addition to smaller changes like introducing a new syntax to accomodate
SBML Level 3's new event features, the principle change with version 2.0
is the ability to translate CellML models, maintaining their modularity in
Antimony's native modularity format.

For version 2.1-beta, the principle change is the ability to produce SBML
models that use the proposed 'Hierarchical Model Composition' package
constructs. This feature uses the 'sbml-comp' package code written for
libSBML (by yours truly) and can hopefully serve as an example both of how
to write code using this package, as well as now providing the ability to
produce actual hierarchical models in the proposed format. QTAntimony
v2.1-beta allows you to view the SBML models in 'comp' and in 'flattened'
form. From the SBML model tab, select 'Edit/Flatten SBML tab(s)' (or hit
Control-F) to toggle between the two modes.

The fact that v2.1 is currently in beta is a reflection of the fact that
the 'comp' package proposal has not yet been finalized, and changes to the
format may still occur which may invalidate models produced with this
tool. Nonetheless, the models should be instructive to those interested
in the comp package.

Antimony now uses CMake as its build system, which hopefully will make
compilation on a variety of platforms more straightforward.


=======================
What was it originally?
=======================

Antimony is a modular, human-readable, human-writeable model definition
language, originally based off of Jarnac, and extended to be fully
modular. So named because the chemical symbol for antimony is 'Sb',
Antimony is designed to allow you to rapidly create new SBML models, and
view SBML models in a simplified text form. libAntimony is a library
designed to allow programmers to add interfaces to their software to allow
users to create and view models in this way. It is currently used in the
programs Tinkercell (http://www.tinkercell.com/) and JSim
(http://www.physiome.org/jsim/).

In addition, a simple editor 'QTAntimony' (written in, of all things, QT)
is provided as a way to get started using Antimony on its own. This
editor displays your model using different tabs, each containing a
different translation. It can read and write models written in Antimony,
SBML, and CellML, and can translate between the three formats by simply
clicking on the appropriate tab. A major client of QTAntimony have been
Biomodels.net curators, who have used it to transform models in published
papers to SBML.


==================
Where is it going?
==================

Antimony will continue to be on the leading edge of 'comp' package use
(since the same guy who's writing this program is also writing the
libSBML-comp code), and will probably be one of the two implementations
required to move the package to a 'finalized' status. As such, we will be
adding the concept of deletions to the syntax soon, as well as the concept
of conversion factors (assuming the latter survives to the final draft of
the specification).

In addition, it has long been our desire to add units to the Antimony
syntax, and this is next on our list of Things To Do (tm). Attaching
units to variables should be relatively straightforward, but allowing
users to attach units to constants (as is now allowed in SBML Level 3)
will probably require the development of a brand-new infix parser. If it
does, we may consider donating this code to libsbml on the theory that
others may find it useful as well. Watch this space!


================
Who is to blame?
================

Antimony was developed by Lucian Smith from an original specification
developed by Dr. Herbert Sauro and Frank Bergmann, under a grant from the
NIH (thanks, the NIH!). It uses libSBML
(http://sbml.org/Software/libSBML), the CellML API
(http://www.cellml.org/tools/api), and the QT libraries
(http://qt.nokia.com/).


========================================
Do I get something for reading this far?
========================================

My undying gratitude. And you get to read the joke footnote, below!



Thank you!

-Lucian Smith


*(for values of 'We are' equal to 'I am'. But using 'we' makes it sound
more distinguished, don't you think?)

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• [cellml-discussion] New release of Antimony v2.0 and v2.1-beta, Lucian Smith, 09/23/2011

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