Related references
Note: Only part of the references are listed.SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating et al.
MOLECULAR SYSTEMS BIOLOGY (2020)
Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization
Niccolo Totis et al.
COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS, CIBB 2018 (2020)
ginSODA: massive parallel integration of stiff ODE systems on GPUs
Marco S. Nobile et al.
JOURNAL OF SUPERCOMPUTING (2019)
Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design
Andrea Tangherloni et al.
APPLIED SOFT COMPUTING (2019)
A strongly S-stable low-dissipation and low-dispersion Runge-Kutta scheme for convection diffusion systems
Yongle Du et al.
AEROSPACE SCIENCE AND TECHNOLOGY (2019)
Fuzzy Self-Tuning PSO: A settings-free algorithm for global optimization
Marco S. Nobile et al.
SWARM AND EVOLUTIONARY COMPUTATION (2018)
Computational Intelligence for Parameter Estimation of Biochemical Systems
Marco S. Nobile et al.
2018 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC) (2018)
Gpufit: An open-source toolkit for GPU-accelerated curve fitting
Adrian Przybylski et al.
SCIENTIFIC REPORTS (2017)
GPU-powered model analysis with PySB/cupSODA
Leonard A. Harris et al.
BIOINFORMATICS (2017)
LASSIE: simulating large-scale models of biochemical systems on GPUs
Andrea Tangherloni et al.
BMC BIOINFORMATICS (2017)
BioNetGen 2.2: advances in rule-based modeling
Leonard A. Harris et al.
BIOINFORMATICS (2016)
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
Brian Drawert et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
libRoadRunner: a high performance SBML simulation and analysis library
Endre T. Somogyi et al.
BIOINFORMATICS (2015)
150 Years of the Mass Action Law
Eberhard O. Voit et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Acceleration of discrete stochastic biochemical simulation using GPGPU
Kei Sumiyoshi et al.
FRONTIERS IN PHYSIOLOGY (2015)
Computational Analysis of an Autophagy/Translation Switch Based on Mutual Inhibition of MTORC1 and ULK1
Paulina Szymanska et al.
PLOS ONE (2015)
GPU-accelerated simulations of mass-action kinetics models with cupSODA
Marco S. Nobile et al.
JOURNAL OF SUPERCOMPUTING (2014)
cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems
Marco S. Nobile et al.
PLOS ONE (2014)
Stochastic simulation in systems biology
Tamas Szekely et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2014)
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes
Kieran Smallbone et al.
FEBS LETTERS (2013)
Understanding Metabolic Regulation and Its Influence on Cell Physiology
Christian M. Metallo et al.
MOLECULAR CELL (2013)
Programming biological models in Python using PySB
Carlos F. Lopez et al.
MOLECULAR SYSTEMS BIOLOGY (2013)
Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units
Ivan Komarov et al.
PLOS ONE (2012)
Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units
Ivan Komarov et al.
PLOS ONE (2012)
GPU accelerated biochemical network simulation
Yanxiang Zhou et al.
BIOINFORMATICS (2011)
Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models
Neema Jamshidi et al.
BIOPHYSICAL JOURNAL (2010)
Variance based sensitivity analysis of model output. Design and estimator for the total sensitivity index
Andrea Saltelli et al.
COMPUTER PHYSICS COMMUNICATIONS (2010)
A 17th-order Radau IIA method for package RADAU. Applications in mechanical systems
J. Martin-Vaquero
COMPUTERS & MATHEMATICS WITH APPLICATIONS (2010)
EFFICIENT PARALLELIZATION OF THE STOCHASTIC SIMULATION ALGORITHM FOR CHEMICALLY REACTING SYSTEMS ON THE GRAPHICS PROCESSING UNIT
Hong Li et al.
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS (2010)
Modeling and Analysis of Mass-Action Kinetics NONNEGATIVITY, REALIZABILITY, REDUCIBILITY, AND SEMISTABILITY
Vijaysekhar Chellaboina et al.
IEEE CONTROL SYSTEMS MAGAZINE (2009)
Recent developments in parameter estimation and structure identification of biochemical and genomic systems
I-Chun Chou et al.
MATHEMATICAL BIOSCIENCES (2009)
Stochastic modelling for quantitative description of heterogeneous biological systems
Darren J. Wilkinson
NATURE REVIEWS GENETICS (2009)
Virtual Cell modelling and simulation software environment
I. I. Moraru et al.
IET SYSTEMS BIOLOGY (2008)
Sensitivity Analysis and Robust Experimental Design of a Signal Transduction Pathway System
Hong Yue et al.
INTERNATIONAL JOURNAL OF CHEMICAL KINETICS (2008)
Metabolic gene regulation in a dynamically changing environment
Matthew R. Bennett et al.
NATURE (2008)
Kinetic parameters and lactate dehydrogenase isozyme activities support possible lactate utilization by neurons
Janet O'Brien et al.
NEUROCHEMICAL RESEARCH (2007)
Stochastic simulation of chemical kinetics
Daniel T. Gillespie
ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2007)
COPASI- A COmplex PAthway SImulator
Stefan Hoops et al.
BIOINFORMATICS (2006)
Physicochemical modelling of cell signalling pathways
Bree B. Aldridge et al.
NATURE CELL BIOLOGY (2006)
A partitioned leaping approach for multiscale modeling of chemical reaction dynamics
Leonard A. Harris et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Efficient step size selection for the tau-leaping simulation method
Y Cao et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method
M Rathinam et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Making best use of model evaluations to compute sensitivity indices
A Saltelli
COMPUTER PHYSICS COMMUNICATIONS (2002)
Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates
IM Sobol
MATHEMATICS AND COMPUTERS IN SIMULATION (2001)
Share Paper
