Simmune specifications


Unique identifier OMICS_06965
Name Simmune
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes


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Publication for Simmune

Simmune in publications

PMCID: 5702122
PMID: 29178887
DOI: 10.1186/s12918-017-0491-4

[…] into account the coarse-grained structural details of protein molecules [, ]. however, most of the early rbm tools were developed aiming at non-spatial modeling. recently, the rbm tools kappa [], simmune [], and bionetgen [] are being added with new capabilities for spatiotemporal modeling. the molecular dynamics (md) simulation is used to model protein structures with atomistic details []. […]

PMCID: 4977479
PMID: 27490268
DOI: 10.1186/s12918-016-0294-z

[…] are associated with the same rate law. the rules can usually be specified independently. rule-based specification methods include kappa-calculus [], bionetgen [], anc [], and ml-rules []. the simmune project and the ssc allow the specification of molecules within spatial regions of arbitrary geometries []., bionetgen [] is a popular rule-based modeling software which uses graph rewriting. […]

PMCID: 4839115
PMID: 27098278
DOI: 10.1186/s12918-016-0275-2

[…] [] and pharmacokinetic/pharmacodynamic modeling of antibiotics []., there are many software packages for simulation of the immune system in various capacities. these include packages such as simmune [], the basic immune simulator [], simisys [], and c-immsim [–]. these packages are general-purpose immune system simulators that, while effective and useful for their intended purposes, […]

PMCID: 4705510
PMID: 26329787
DOI: 10.1186/1471-2105-16-S12-S2

[…] knowledge of mathematical equations can utilize copasi to model complex networks. copasi currently supports only ode-based models. for agent-based modeling, there are several existing tools such as simmune [] and basic immune simulator, bis []; however, these are not designed to be easily extended to developing multiscale models of enteric immune systems. for generic modeling framework, […]

PMCID: 4201162
PMID: 25254957
DOI: 10.1371/journal.pcbi.1003844

[…] and simulation tools have been designed to accommodate spatial heterogeneity in order to allow for the realistic simulation of interactions within biological compartments. for instance, the simmune project , includes a spatial component: users can specify their multi-state biomolecules and interactions within membranes or compartments of arbitrary shape. the reaction volume […]

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Simmune institution(s)
Computational Biology Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA

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