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BioNetGen

swMATH ID: 9072
Software Authors: Blinov, Michael L.; Faeder, James R.; Goldstein, Byron; Hlavacek, William S.
Description: BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts comprehensively and precisely for specified enzymatic activities, potential post-translational modifications and interactions of the domains of signaling molecules. The output defines and parameterizes the network of molecular species that can arise during signaling and provides functions that relate model variables to experimental readouts of interest. Models that can be generated are relevant for rational drug discovery, analysis of proteomic data and mechanistic studies of signal transduction.
Homepage: http://bionetgen.org/index.php/Main_Page
Related Software: Bio-PEPA; NFsim; COPASI; PySB; BIOCHAM; LBS; Python; PRISM; libSBML; ERODE; RuleBender; Haskell; KaDE; BlenX; PEPA; libRoadRunner; BioModels; Chromar; GitHub; SpiCO
Cited in: 68 Documents
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Cited by 161 Authors

9 Feret, Jérôme
5 Honorato-Zimmer, Ricardo
5 Tribastone, Mirco
5 Tschaikowski, Max
5 Vandin, Andrea
4 Petrov, Tatjana
3 Boutillier, Pierre
3 Brim, Luboš
3 Cardelli, Luca
3 Danos, Vincent
3 Koeppl, Heinz
3 Šafránek, David
3 Troják, Matej
2 Behr, Nicolas
2 Calder, Muffy
2 Camporesi, Ferdinanda
2 Czeizler, Eugen
2 Degasperi, Andrea
2 Faeder, James R.
2 Hlavacek, William S.
2 Jaramillo-Riveri, Sebastián
2 Krivine, Jean
2 Lhoussaine, Cédric
2 Lipniacki, Tomasz
2 Millar, Andrew J.
2 Plotkin, Gordon D.
2 Šalagovič, Jakub
2 Stucki, Sandro
2 Uhrmacher, Adelinde M.
2 Warnke, Tom
2 Winfree, Erik
2 Zardilis, Argyris
1 Aguilar-Ibáñez, Carlos Fernando
1 Álvarez-Buylla, Elena R.
1 Alvarez, Robinson F.
1 Aman, Bogdan
1 Amărioarei, Alexandru
1 An, Gary
1 Barad, Gefry
1 Barbuto, José A. M.
1 Barua, Dipak
1 Bazzazi, Hojjat
1 Beica, Andreea
1 Blanc, Emilie
1 Blinov, Michael L.
1 Boreale, Michele
1 Brozmann, Branislav
1 Cantrell, Doreen A.
1 Červený, Jan
1 Cess, Colin G.
1 Chiarugi, Davide
1 Ciobanu, Gabriel
1 Clermont, Gilles
1 Constantine, Gregory M.
1 Crampin, Edmund John
1 Cravo, Fabricio
1 Cristescu, Ioana Domnina
1 Csete, Marie
1 Czeizler, Elena
1 De Maria, Elisabetta
1 Děd, T.
1 Dobre, Ana-Maria
1 Eftimie, Raluca
1 Ehrhard, Thomas
1 Elston, Timothy C.
1 Engblom, Stefan
1 Erickson, Keesha E.
1 Ermentrout, George Bard
1 Fages, François
1 Falaschi, Moreno
1 Faure de Pebeyre, Aurélie
1 Feng, Song
1 Fernández, Maribel
1 Finley, Stacey D.
1 Függer, Matthias
1 Ganguly, Arnab
1 Garay-Arroyo, Adriana
1 Gillard, Joseph J.
1 Glazier, James A.
1 Harmer, Russ
1 Harmer, Russell S.
1 Hat, Beata
1 Hayman, Jonathan Mark
1 Hellander, Andreas
1 Helms, Tobias
1 Henzinger, Thomas A.
1 Hermith, Diana
1 Iţcuş, Corina
1 Jafarnejad, Mohammad
1 Jiménez-Pastor, Antonio
1 John, Mathias
1 Kaufmann, William K.
1 Kesseler, Kevin J.
1 Khan, Raheel
1 Khetan, Jawahar
1 Kirchner, Hélène
1 Kirste, Thomas
1 Klement, M.
1 Kocieniewski, PaweŁ
1 Kraikivski, Pavel
...and 61 more Authors
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Cited in 13 Serials

11 Journal of Theoretical Biology
9 Theoretical Computer Science
3 Mathematical Biosciences
2 Bulletin of Mathematical Biology
2 Logical Methods in Computer Science
2 Journal of Logical and Algebraic Methods in Programming
1 Journal of Mathematical Biology
1 Cybernetics and Systems Analysis
1 The Journal of Artificial Intelligence Research (JAIR)
1 ACM Transactions on Modeling and Computer Simulation
1 Natural Computing
1 Multiscale Modeling & Simulation
1 Discrete Mathematics, Algorithms and Applications
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Cited in 16 Fields

55 Biology and other natural sciences (92-XX)
34 Computer science (68-XX)
5 Ordinary differential equations (34-XX)
4 Probability theory and stochastic processes (60-XX)
3 Systems theory; control (93-XX)
2 Combinatorics (05-XX)
1 Mathematical logic and foundations (03-XX)
1 Commutative algebra (13-XX)
1 Category theory; homological algebra (18-XX)
1 Partial differential equations (35-XX)
1 Calculus of variations and optimal control; optimization (49-XX)
1 Numerical analysis (65-XX)
1 Classical thermodynamics, heat transfer (80-XX)
1 Quantum theory (81-XX)
1 Operations research, mathematical programming (90-XX)
1 Game theory, economics, finance, and other social and behavioral sciences (91-XX)

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