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 beta 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.

Are supported antimony features	Antimony features which hadn't supported in beta-version
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;	Declaration "DNA strand definitions" isn't supported, From symbol types only "species" and "compartment" are supported, Reactions with interactions (inhibition, activation) don't use;
Necessary additions in the antimony specification
Algebraic rules Opportunity to divide initial value and initial assignment Opportunity to change independently attributes "constant" and "boundary conditional",

Composite model

Use model definition or external model for adding subdiagram.

Use parameters of subdiagram or synchronization for adding connection.

In the beta-version plugin new declarations were added for working with composite models. If antimony text contains few models or declarations outside model then this text correspond composite model. Main model will be created and it contains all models like model definitions.

Are supported antimony features	Features which aren't supported in beta version
Model definitions, External models, SubDiagrams, Replacing elements from different models;	Sign < * > for defining main model isn't supported, Replacing on elements which are located below in more than one level Example: s1 is A.B.s2, Replacing elements which have different types, Can import only diagram from the current collection, Substitutional elements must be registered in model parameters;
New elements which we added in Antimony language
Prefix for different type ports: contact: "a", input: ">a", output: "<a"; Example: model nameModel(a,<b,>c);

See also

• Visual modeling