Antimony

Antimony plugin

Visual (SBGN) and text-based (Antimony) representations of SBML model in BioUML

Antimony plugin for BioUML 0.9.6 aims to combine two representations of mathematical model (particularly - SBML model):

• visual representation as BioUML-diagram using extended SBGN notation
• text-based representation using Antimony language.

Plugin allows user to edit model both visually and as text. If visual repesentation is changed - antimony text is updated on the fly.
Text changes are applied to the diagram on demand (after pressing "Apply Antimony" button).
Besides model representations syncrhonisation, we also try to presereve user diagram layout as well as antimony text format (spaces, comments, etc.)
Please note: antimony changes will be applied to the diagram only after "Apply Antimony" button is pressed. If you change diagram before you press this button, all changes in text will be lost!

Scheme for compartment adding via Antimony

Scheme for species adding via Antimony

Features overview

Currently plugin is in alpha version, some features of antimony aren't supported. Also we want to achieve full synchronization between antimony and sbml-model in BioUML. And for this purpose we need some additions for the antimony specification.

Supported within an antimony	Necessary additions in the antimony specification
Creating and removal of species, compartments, Putting nodes into parental compartments, Changing initial values, Creating and removal of reaction with reactants and products, Editing kinetic laws of reactions, Creating, removal and editing of functions, Creating, removal and editing of scalar and rate equations, Mounting constant value for species and variables;	Algebraic rules Opportunity to divide initial value and initial assignment Opportunity to change independently attributes "constant" and "boundary conditional", "Delay" for events;
Antimony features which hadn't supported in alfa-version
Import statements don't supported, All declarations must be inside only one model, Model can't have parameters, Some declarations don't supported: imported models, DNA strand definitions, synchronizations, deletions, display names, From symbol types only "species" and "compartment" are supported, Reactions with interactions (inhibition, activation) don't use, Also events and initial assignments work incorrectly;

See also

• Visual modeling