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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


No version available

Publication for Simmune

Simmune citations


A multiscale modeling study of particle size effects on the tissue penetration efficacy of drug delivery nanoparticles

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

[…] ing 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 []. Bu […]


Extending rule based methods to model molecular geometry and 3D model resolution

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

[…] actions 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. Th […]


A computational model of invasive aspergillosis in the lung and the role of iron

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

[…] diffusion [] 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, are u […]


Multiscale modeling of mucosal immune responses

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

[…] d 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, computat […]


MOSBIE: a tool for comparison and analysis of rule based biochemical models

BMC Bioinformatics
PMCID: 4261755
PMID: 25253680
DOI: 10.1186/1471-2105-15-316

[…] r both similarities and differences in their structure.Although several software tools have been developed for interactive visualization of rule-based models, including RuleBender [–], rxncon [], and Simmune NetworkViewer [], these tools aim to assist in viewing and understanding one model at a time and do not directly support model comparison, the focus of the current work. As we discuss in more […]


Multi state Modeling of Biomolecules

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

[…] eneration 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 is then divi […]


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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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