Antimony specifications

Information


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

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Maintainer


  • person_outline Lucian P. Smith <>

Publications for Antimony

Antimony in publications

 (6)
PMCID: 4456403
PMID: 26043208
DOI: 10.1371/journal.pone.0114296

[…] using javascript. the formal foundations of the script language construct are outlined in subsection 4.5., we discuss related work in the first subsection before finally concluding., 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 […]

PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] this young format (olivier et al., ; myers et al., ; kolpakov et al., ; keller et al., ). a workflow editor (sed-ed), api libraries (libsedml, jlibsedml), and a simplified scripting language (antimony) are also available (smith et al., ; adams, )., the visual representation of biochemical pathways has a long tradition. displays of biological circuit diagrams and reaction pathways […]

PMCID: 4183381
PMID: 25275523
DOI: 10.1371/journal.pcbi.1003849

[…] 1 compositions, the modeler establishes links between models by creating mappings between code-level constructs such as model variables. technologies that support this type of composition include antimony (http://antimony.sourceforge.net), the systems biology markup language (sbml) hierarchical model composition package […]

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

[…] 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 […]

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

[…] 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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