NFsim statistics

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NFsim specifications

Information


Unique identifier OMICS_06961
Name NFsim
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for NFsim

NFsim in publications

 (14)
PMCID: 5860782
PMID: 29518071
DOI: 10.1371/journal.pcbi.1006022

[…] the arp2/3 complex and a simplified vesicle forming protein subset. simulating higher complex formation is challenging because of the exponentially large number of possible species, so we used nfsim[], a stochastic solver of chemical kinetics that is rule-based, enabling an efficient tracking of higher-order complexes as they appear in time., one unexpected imbalance we found […]

PMCID: 5264505
PMID: 27903820
DOI: 10.1042/EBC20160037

[…] of relevance to the cell biology and desired population-level features. furthermore, the integration of tools designed to efficiently model the reaction networks inside cells (e.g. smoldyn [] or nfsim []), and the application of whole-cell models [] to provide detailed behavioural responses would enable accurate simulations. at present, most tools do not provide these features due […]

PMCID: 5516868
PMID: 28725459
DOI: 10.1038/npjsba.2015.7

[…] language (). the resulting model has 176 distinct parameters, precluding reliable parameter estimation based on current data and hence meaningful analysis. however, the model can be simulated using nfsim, demonstrating that the rxncon network reconstruction can be used as basis for dynamic simulations., here, we present a network reconstruction of the snf1 signalling pathway. network […]

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

[…] the software in java, c++ or any other programming language. in addition, there are also several existing agent-based immune simulators, including simmune [], parimm [], immsim [], sis [], and nfsim [], that have been developed over the past decade. for instance, simmune is a modeling environment where cell-cell and cell-molecule interactions could lead to an adaptive behavior […]

PMCID: 4447392
PMID: 26020242
DOI: 10.1371/journal.pcbi.1004246

[…] and predict senescence for different temporal patterns of irradiation [,]. the integrated model was built in rule-based format in bionetgen [–] and for simulation we used the network-free simulator nfsim [], which lead to a considerable reduction in computation time. we show that the model is able to explain the long-term decrease in dna damage repair and also to predict experimental results […]


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NFsim institution(s)
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA

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