These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
3. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. van Riel NA Brief Bioinform; 2006 Dec; 7(4):364-74. PubMed ID: 17107967 [TBL] [Abstract][Full Text] [Related]
4. Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Montagud A; Traynard P; Martignetti L; Bonnet E; Barillot E; Zinovyev A; Calzone L Brief Bioinform; 2019 Jul; 20(4):1238-1249. PubMed ID: 29237040 [TBL] [Abstract][Full Text] [Related]
5. PeTTSy: a computational tool for perturbation analysis of complex systems biology models. Domijan M; Brown PE; Shulgin BV; Rand DA BMC Bioinformatics; 2016 Mar; 17():124. PubMed ID: 26964749 [TBL] [Abstract][Full Text] [Related]
6. Learning (from) the errors of a systems biology model. Engelhardt B; Frőhlich H; Kschischo M Sci Rep; 2016 Feb; 6():20772. PubMed ID: 26865316 [TBL] [Abstract][Full Text] [Related]
7. Maximally informative next experiments for nonlinear models. McGee RL; Buzzard GT Math Biosci; 2018 Aug; 302():1-8. PubMed ID: 29709517 [TBL] [Abstract][Full Text] [Related]
8. Experimental design for dynamics identification of cellular processes. Dinh V; Rundell AE; Buzzard GT Bull Math Biol; 2014 Mar; 76(3):597-626. PubMed ID: 24522560 [TBL] [Abstract][Full Text] [Related]
9. On the selection of ordinary differential equation models with application to predator-prey dynamical models. Zhang X; Cao J; Carroll RJ Biometrics; 2015 Mar; 71(1):131-138. PubMed ID: 25287611 [TBL] [Abstract][Full Text] [Related]
10. Experimental Design for Stochastic Models of Nonlinear Signaling Pathways Using an Interval-Wise Linear Noise Approximation and State Estimation. Zimmer C PLoS One; 2016; 11(9):e0159902. PubMed ID: 27583802 [TBL] [Abstract][Full Text] [Related]
11. Computational procedures for optimal experimental design in biological systems. Balsa-Canto E; Alonso AA; Banga JR IET Syst Biol; 2008 Jul; 2(4):163-72. PubMed ID: 18681746 [TBL] [Abstract][Full Text] [Related]
12. A toolbox for discrete modelling of cell signalling dynamics. Paterson YZ; Shorthouse D; Pleijzier MW; Piterman N; Bendtsen C; Hall BA; Fisher J Integr Biol (Camb); 2018 Jun; 10(6):370-382. PubMed ID: 29855020 [TBL] [Abstract][Full Text] [Related]
13. Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment. Steiert B; Kreutz C; Raue A; Timmer J Methods Mol Biol; 2019; 1945():341-362. PubMed ID: 30945255 [TBL] [Abstract][Full Text] [Related]
14. 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]
15. CRA toolbox: software package for conditional robustness analysis of cancer systems biology models in MATLAB. Bianconi F; Antonini C; Tomassoni L; Valigi P BMC Bioinformatics; 2019 Jul; 20(1):385. PubMed ID: 31288758 [TBL] [Abstract][Full Text] [Related]
16. PANSYM: a symbolic equation generator for mathematical modelling, analysis and control of metabolic and pharmacokinetic systems. Thomaseth K Comput Methods Programs Biomed; 1994 Feb; 42(2):99-112. PubMed ID: 8205801 [TBL] [Abstract][Full Text] [Related]
17. A Bayesian approach to estimating hidden variables as well as missing and wrong molecular interactions in ordinary differential equation-based mathematical models. Engelhardt B; Kschischo M; Fröhlich H J R Soc Interface; 2017 Jun; 14(131):. PubMed ID: 28615495 [TBL] [Abstract][Full Text] [Related]
18. Realistic simulation of time-course measurements in systems biology. Egert J; Kreutz C Math Biosci Eng; 2023 Apr; 20(6):10570-10589. PubMed ID: 37322949 [TBL] [Abstract][Full Text] [Related]
19. 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]