
sbioPN
 Referenced in 5 articles
[sw11725]
 sbioPN: Simulation of deterministic and stochastic spatial biochemical reaction networks using Petri Nets. sbioPN ... perform simulation of deterministic and stochastic systems of biochemical reaction networks with spatial effects. Models ... deterministic solutions, sbioPN creates the associated system of differential equations ”on the fly”, and solves...

PhysiCell
 Referenced in 10 articles
[sw30634]
 virtual laboratory” for such multicellular systems simulates both the biochemical microenvironment (the ”stage”) and many ... mechanically and biochemically interacting cells (the ”players” upon the stage). PhysiCellphysicsbased multicellular simulator ... PhysiCell with examples in synthetic multicellular systems (a ”cellular cargo delivery” system, with application...

SABRE
 Referenced in 7 articles
[sw12884]
 analysis of biochemical reaction networks. The importance of stochasticity within biological systems has been shown ... SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization ... biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level...

ECELL
 Referenced in 23 articles
[sw07917]
 environment for biochemical and genetic processes, has been developed. The ECELL system allows...

iNA
 Referenced in 4 articles
[sw17973]
 exploration of stochastic biochemical kinetics using the system size expansion. The accepted stochastic descriptions ... biochemical dynamics under wellmixed conditions are given by the Chemical Master Equation ... difference equations for the probability of the system being in any one of the possible ... analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion...

NFsim
 Referenced in 11 articles
[sw22256]
 free, opensource, biochemical reaction simulator designed to handle systems that have a large...

Charlie
 Referenced in 4 articles
[sw12881]
 model validation of natural systems, i.e. biochemical networks, such as metabolic, signal transduction, and gene...

Memtype2L
 Referenced in 39 articles
[sw16472]
 process with other molecules in a biological system. Particularly, with the avalanche of protein sequences ... relatively much slower progress in using biochemical experiments to determine their functions, it is highly...

AAindex
 Referenced in 47 articles
[sw26861]
 numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino ... database may be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.ad. jp/dbget...

SCAMP
 Referenced in 11 articles
[sw02112]
 systems that support an ANSI C compiler. SCAMP accepts metabolic models described in a biochemical ... users rapidly to build and simulate metabolic systems. The language is sufficiently flexible to enable...

Path2Models
 Referenced in 4 articles
[sw29332]
 generation of computational models from biochemical pathway maps. Background: Systems biology projects and omics technologies...

Facile
 Referenced in 1 article
[sw28767]
 biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions ... systems biology model. Facile implements the law of mass action to automatically compile a biochemical...

iMethylPseAAC
 Referenced in 21 articles
[sw22443]
 predictor, called iMethylPseAAC. In the prediction system, a peptide sample was formulated ... formed by incorporating its physicochemical, sequence evolution, biochemical, and structural disorder information into the general...

BSTLab
 Referenced in 1 article
[sw33332]
 BSTLab: A Matlab Toolbox for Biochemical Systems Theory. The toolbox, BSTLab, implements functions common...

Compartor
 Referenced in 1 article
[sw41452]
 stochastic dynamics of a compartmentalized biochemical system can be effectively studied using moment equations. With...

GillesPy2
 Referenced in 1 article
[sw38638]
 Python package for stochastic simulation of biochemical systems. It offers an objectoriented approach...

LASSIE
 Referenced in 1 article
[sw29330]
 LASSIE: simulating largescale models of biochemical systems on GPUs. Results: LASSIE is a “black...

HSimulator
 Referenced in 2 articles
[sw22841]
 multithread simulator for massaction biochemical reaction systems placed in a wellmixed environment. HSimulator...

Data2Dynamics
 Referenced in 12 articles
[sw25272]
 popular approach in the field of systems biology. Two of the most critical steps ... approach are to construct dynamical models of biochemical reaction networks for large datasets and complex ... differential equations and of the associated sensitivity system are parallelized and automatically compiled into efficient...

Smoldyn
 Referenced in 23 articles
[sw23962]
 computer program for cellscale biochemical simulations. It simulates each molecule of interest individually ... they would in a real biological system. Smoldyn is easy to use and easy...