232 related articles for article (PubMed ID: 22727185)
21. Hybrid deterministic/stochastic simulation of complex biochemical systems.
Lecca P; Bagagiolo F; Scarpa M
Mol Biosyst; 2017 Nov; 13(12):2672-2686. PubMed ID: 29058744
[TBL] [Abstract][Full Text] [Related]
22. Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).
Hafner J
J Phys Condens Matter; 2008 Feb; 20(6):060301. PubMed ID: 21693862
[TBL] [Abstract][Full Text] [Related]
23. Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent.
Wang Y; Christley S; Mjolsness E; Xie X
BMC Syst Biol; 2010 Jul; 4():99. PubMed ID: 20663171
[TBL] [Abstract][Full Text] [Related]
24. CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.
Kazeroonian A; Fröhlich F; Raue A; Theis FJ; Hasenauer J
PLoS One; 2016; 11(1):e0146732. PubMed ID: 26807911
[TBL] [Abstract][Full Text] [Related]
25. Spatial and stochastic cellular modeling with the Smoldyn simulator.
Andrews SS
Methods Mol Biol; 2012; 804():519-42. PubMed ID: 22144170
[TBL] [Abstract][Full Text] [Related]
26. Vivarium: an interface and engine for integrative multiscale modeling in computational biology.
Agmon E; Spangler RK; Skalnik CJ; Poole W; Peirce SM; Morrison JH; Covert MW
Bioinformatics; 2022 Mar; 38(7):1972-1979. PubMed ID: 35134830
[TBL] [Abstract][Full Text] [Related]
27. Vesicle and reaction-diffusion hybrid modeling with STEPS.
Hepburn I; Lallouette J; Chen W; Gallimore AR; Nagasawa-Soeda SY; De Schutter E
Commun Biol; 2024 May; 7(1):573. PubMed ID: 38750123
[TBL] [Abstract][Full Text] [Related]
28. MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.
Cai JJ; Smith DK; Xia X; Yuen KY
BMC Bioinformatics; 2005 Mar; 6():64. PubMed ID: 15780146
[TBL] [Abstract][Full Text] [Related]
29. Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.
Pischel D; Sundmacher K; Flassig RJ
Bioinformatics; 2017 Jul; 33(14):i319-i324. PubMed ID: 28881987
[TBL] [Abstract][Full Text] [Related]
30. BioSimulator.jl: Stochastic simulation in Julia.
Landeros A; Stutz T; Keys KL; Alekseyenko A; Sinsheimer JS; Lange K; Sehl ME
Comput Methods Programs Biomed; 2018 Dec; 167():23-35. PubMed ID: 30501857
[TBL] [Abstract][Full Text] [Related]
31. IDESS: a toolbox for identification and automated design of stochastic gene circuits.
Sequeiros C; Pájaro M; Vázquez C; Banga JR; Otero-Muras I
Bioinformatics; 2023 Nov; 39(11):. PubMed ID: 37988145
[TBL] [Abstract][Full Text] [Related]
32. The two-regime method for optimizing stochastic reaction-diffusion simulations.
Flegg MB; Chapman SJ; Erban R
J R Soc Interface; 2012 May; 9(70):859-68. PubMed ID: 22012973
[TBL] [Abstract][Full Text] [Related]
33. A scalable moment-closure approximation for large-scale biochemical reaction networks.
Kazeroonian A; Theis FJ; Hasenauer J
Bioinformatics; 2017 Jul; 33(14):i293-i300. PubMed ID: 28881983
[TBL] [Abstract][Full Text] [Related]
34. SELANSI: a toolbox for simulation of stochastic gene regulatory networks.
Pájaro M; Otero-Muras I; Vázquez C; Alonso AA
Bioinformatics; 2018 Mar; 34(5):893-895. PubMed ID: 29040384
[TBL] [Abstract][Full Text] [Related]
35. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.
Stoma S; Fröhlich M; Gerber S; Klipp E
BMC Bioinformatics; 2011 Apr; 12():126. PubMed ID: 21527030
[TBL] [Abstract][Full Text] [Related]
36. Probability distributed time delays: integrating spatial effects into temporal models.
Marquez-Lago TT; Leier A; Burrage K
BMC Syst Biol; 2010 Mar; 4():19. PubMed ID: 20202198
[TBL] [Abstract][Full Text] [Related]
37. Efficient Constant-Time Complexity Algorithm for Stochastic Simulation of Large Reaction Networks.
Thanh VH; Zunino R; Priami C
IEEE/ACM Trans Comput Biol Bioinform; 2017; 14(3):657-667. PubMed ID: 26890923
[TBL] [Abstract][Full Text] [Related]
38. Multiresolution stochastic simulations of reaction-diffusion processes.
Bayati B; Chatelain P; Koumoutsakos P
Phys Chem Chem Phys; 2008 Oct; 10(39):5963-6. PubMed ID: 18825283
[TBL] [Abstract][Full Text] [Related]
39. EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology.
Picault S; Huang YL; Sicard V; Arnoux S; Beaunée G; Ezanno P
PLoS Comput Biol; 2019 Sep; 15(9):e1007342. PubMed ID: 31518349
[TBL] [Abstract][Full Text] [Related]
40. Three-dimensional stochastic simulation of chemoattractant-mediated excitability in cells.
Biswas D; Devreotes PN; Iglesias PA
PLoS Comput Biol; 2021 Jul; 17(7):e1008803. PubMed ID: 34260581
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]
