162 related articles for article (PubMed ID: 28754122)
1. Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.
Herajy M; Liu F; Rohr C; Heiner M
BMC Syst Biol; 2017 Jul; 11(1):71. PubMed ID: 28754122
[TBL] [Abstract][Full Text] [Related]
2. Snoopy--a unifying Petri net framework to investigate biomolecular networks.
Rohr C; Marwan W; Heiner M
Bioinformatics; 2010 Apr; 26(7):974-5. PubMed ID: 20139470
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks.
Adalsteinsson D; McMillen D; Elston TC
BMC Bioinformatics; 2004 Mar; 5():24. PubMed ID: 15113411
[TBL] [Abstract][Full Text] [Related]
5. MONALISA for stochastic simulations of Petri net models of biochemical systems.
Balazki P; Lindauer K; Einloft J; Ackermann J; Koch I
BMC Bioinformatics; 2015 Jul; 16():215. PubMed ID: 26156221
[TBL] [Abstract][Full Text] [Related]
6. Coloured Hybrid Petri Nets: An adaptable modelling approach for multi-scale biological networks.
Herajy M; Liu F; Rohr C; Heiner M
Comput Biol Chem; 2018 Oct; 76():87-100. PubMed ID: 29982167
[TBL] [Abstract][Full Text] [Related]
7. Petri nets in Snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks.
Marwan W; Rohr C; Heiner M
Methods Mol Biol; 2012; 804():409-37. PubMed ID: 22144165
[TBL] [Abstract][Full Text] [Related]
8. pSSAlib: The partial-propensity stochastic chemical network simulator.
Ostrenko O; Incardona P; Ramaswamy R; Brusch L; Sbalzarini IF
PLoS Comput Biol; 2017 Dec; 13(12):e1005865. PubMed ID: 29206229
[TBL] [Abstract][Full Text] [Related]
9. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions.
Salis H; Kaznessis Y
J Chem Phys; 2005 Feb; 122(5):54103. PubMed ID: 15740306
[TBL] [Abstract][Full Text] [Related]
10. Petri net modelling of gene regulation of the Duchenne muscular dystrophy.
Grunwald S; Speer A; Ackermann J; Koch I
Biosystems; 2008 May; 92(2):189-205. PubMed ID: 18372101
[TBL] [Abstract][Full Text] [Related]
11. Modelling and simulating reaction-diffusion systems using coloured Petri nets.
Liu F; Blätke MA; Heiner M; Yang M
Comput Biol Med; 2014 Oct; 53():297-308. PubMed ID: 25150626
[TBL] [Abstract][Full Text] [Related]
12. Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions.
Alexiou A; Chatzichronis S; Perveen A; Hafeez A; Ashraf GM
Curr Top Med Chem; 2019; 19(6):413-425. PubMed ID: 30854971
[TBL] [Abstract][Full Text] [Related]
13. PetriScape - A plugin for discrete Petri net simulations in Cytoscape.
Almeida D; Azevedo V; Silva A; Baumbach J
J Integr Bioinform; 2016 Jun; 13(1):284. PubMed ID: 27402693
[TBL] [Abstract][Full Text] [Related]
14. Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes.
Sedwards S; Mazza T
Bioinformatics; 2007 Oct; 23(20):2800-2. PubMed ID: 17855418
[TBL] [Abstract][Full Text] [Related]
15. Multiscale Hy3S: hybrid stochastic simulation for supercomputers.
Salis H; Sotiropoulos V; Kaznessis YN
BMC Bioinformatics; 2006 Feb; 7():93. PubMed ID: 16504125
[TBL] [Abstract][Full Text] [Related]
16. COPASI--a COmplex PAthway SImulator.
Hoops S; Sahle S; Gauges R; Lee C; Pahle J; Simus N; Singhal M; Xu L; Mendes P; Kummer U
Bioinformatics; 2006 Dec; 22(24):3067-74. PubMed ID: 17032683
[TBL] [Abstract][Full Text] [Related]
17. Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.
Radom M; Rybarczyk A; Szawulak B; Andrzejewski H; Chabelski P; Kozak A; Formanowicz P
Bioinformatics; 2017 Dec; 33(23):3822-3823. PubMed ID: 28961696
[TBL] [Abstract][Full Text] [Related]
18. STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies.
Hepburn I; Chen W; Wils S; De Schutter E
BMC Syst Biol; 2012 May; 6():36. PubMed ID: 22574658
[TBL] [Abstract][Full Text] [Related]
19. VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology.
Brinkrolf C; Ochel L; Hofestädt R
Biosystems; 2021 Dec; 210():104531. PubMed ID: 34492317
[TBL] [Abstract][Full Text] [Related]
20. Fast and Precise Emulation of Stochastic Biochemical Reaction Networks With Amplified Thermal Noise in Silicon Chips.
Kim J; Woo SS; Sarpeshkar R
IEEE Trans Biomed Circuits Syst; 2018 Apr; 12(2):379-389. PubMed ID: 29570064
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]