NFsim swMATH ID: 22256 Software Authors: Sneddon MW, Faeder JR, Emonet T Description: NFsim is a free, open-source, biochemical reaction simulator designed to handle systems that have a large or even infinite number of possible molecular interactions or states. NFsim also has advanced and flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms. A publication describing NFsim can be found here. NFsim is ideal for modeling polymerization, aggregation, and cooperative reactions that cannot be handled with traditional stochastic or ODE simulators. Models are specified in the BioNetGen Langauge, providing a powerful model building environment. Note that you can now develop BioNetGen and NFsim models with a graphical interface in rulebender! NFsim runs on Windows, Mac, and Linux. NFsim code is freely available under the MIT License on github: https://github.com/msneddon/nfsim . Please cite NFsim as: Sneddon MW, Faeder JR and Emonet T. Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nature Methods (2011) 8(2):177-83. Homepage: http://michaelsneddon.net/nfsim/ Related Software: BioNetGen; ERODE; GitHub; LBS; Bio-PEPA; BIOCHAM; DiffSharp; LumpingPositiviser; CLUE; Nemo; Hecke; polymake; rxncon; Smoldyn; PySB; KappaTools; Spatkin; TRuML; STOCHSIM; BioModels Cited in: 13 Documents all top 5 Cited by 41 Authors 2 Pogudin, Gleb A. 1 Barua, Dipak 1 Boutillier, Pierre 1 Brim, Luboš 1 Cantrell, Doreen A. 1 Cardelli, Luca 1 Červený, Jan 1 Czeizler, Elena 1 Czeizler, Eugen 1 Danos, Vincent 1 Dura-Bernal, Salvador 1 Eftimie, Raluca 1 Ehrhard, Thomas 1 Erickson, Keesha E. 1 Feng, Song 1 Gillard, Joseph J. 1 Hines, Michael L. 1 Hlavacek, William S. 1 Jacob, Joshua Paul 1 Jiménez-Pastor, Antonio 1 Khetan, Jawahar 1 Koeppl, Heinz 1 Krivine, Jean 1 Lin, Yen Ting 1 Lytton, William W. 1 McDougal, Robert A. 1 Mitra, Eshan D. 1 Mohammed, Abdulmelik 1 Šafránek, David 1 Šalagovič, Jakub 1 Schürmann, Felix 1 Seidenstein, Alexandra H. 1 Stumpf, Michael P. H. 1 Suderman, Ryan 1 Tribastone, Mirco 1 Troják, Matej 1 Tschaikowski, Max 1 Vandin, Andrea 1 Vittadello, Sean T. 1 Wilson-Kanamori, John 1 Zhang, Xingjian Cited in 5 Serials 2 Bulletin of Mathematical Biology 2 Theoretical Computer Science 1 Journal of Mathematical Biology 1 Neural Computation 1 Journal of Theoretical Biology all top 5 Cited in 8 Fields 11 Biology and other natural sciences (92-XX) 5 Computer science (68-XX) 2 Ordinary differential equations (34-XX) 1 Combinatorics (05-XX) 1 Group theory and generalizations (20-XX) 1 Algebraic topology (55-XX) 1 Manifolds and cell complexes (57-XX) 1 Systems theory; control (93-XX) Citations by Year