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Antimony specifications


Unique identifier OMICS_08760
Name Antimony
Software type Framework/Library
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 2.7
Stability Stable
Maintained Yes


No version available


  • person_outline Lucian P. Smith

Publications for Antimony

Antimony citations


Toward community standards and software for whole cell modeling

IEEE Trans Biomed Eng
PMCID: 5451320
PMID: 27305665
DOI: 10.1109/TBME.2016.2560762

[…] odel, (2) drawing pathway diagrams using software tools such as CellDesigner [] and VANTED [], and (3) writing scripts to generate SBML from the diagrams. Other groups used model design tools such as Antimony [], BioUML [], COBRApy [], COPASI [], iBioSim [], and libRoadRunner [] to recode submodels based on the original documentation. A few of the groups encoded submodels by converting the MATLAB […]


A High Level Language for Rule Based Modelling

PLoS One
PMCID: 4456403
PMID: 26043208
DOI: 10.1371/journal.pone.0114296

[…] The languages Antimony and PySB mentioned in the introduction are closely related to LBS-κ in that they both address the problem of modularity in a rule-based setting. Being independently developed, the three langu […]


Improving Collaboration by Standardization Efforts in Systems Biology

Front Bioeng Biotechnol
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] plementation (Miller et al., ) or the graphical modeling environments OpenCell (Lloyd, ) and OpenCOR (Nickerson et al., ). CellML can be inter-converted from and to SBML and to the scripting language Antimony (Schilstra et al., ; Smith et al., ). The rates of change of all components are explicit in CellML. When adding components or connections to a model, these rates of change would need to be up […]


Multistate Model Builder (MSMB): a flexible editor for compact biochemical models

BMC Syst Biol
PMCID: 4234935
PMID: 24708852
DOI: 10.1186/1752-0509-8-42

[…] n of reactions without prior existence of species, but can be configured to warn the user when species are automatically inserted.We know of three tools that support multistate modeling in some form. Antimony [] is a model definition language that allows users to specify parts of the model in a scripting-like language, and then combine these parts to create more complex models. While the ideas of […]


Modular, rule based modeling for the design of eukaryotic synthetic gene circuits

BMC Syst Biol
PMCID: 3680069
PMID: 23705868
DOI: 10.1186/1752-0509-7-42

[…] ign and analysis of synthetic gene circuits are available [-]. They present various features such as simulation environments, connection to DNA-sequence databases, internal languages (e.g. Eugene [], Antimony []), and rule-based grammars [,] for circuit specification and design automation. However, they have been tailored to prokaryotic systems only and none of them implements models for eukaryoti […]


Multiscale Modeling and Data Integration in the Virtual Physiological Rat Project

Ann Biomed Eng
PMCID: 3463790
PMID: 22805979
DOI: 10.1007/s10439-012-0611-7

[…] BML, Table ) leverages the machine-readable reaction-level descriptions of SBML models to automate the merging of multiple models. Other model exchange and merging systems have been developed such as Antimony, System for the Analysis of Biochemical Pathways-Reaction Kinetics (SABIO-RK) and Saint which focus on SBML models or a separate reaction kinetics database in the case of SABIO-RK (Antimony, […]

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Antimony institution(s)
Department of Bioengineering, University of Washington, Seattle, WA, USA
Antimony funding source(s)
National Institutes of Health (grant 1R01GM081070-01); National Science Foundation (grant 0527023-FIBR)

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