Simmune specifications

Information


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

Versioning


Add your version

Publication for Simmune

Simmune in publications

 (10)
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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

Simmune reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Simmune