• 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). PhysiCell-physics-based 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...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • environment for biochemical and genetic processes, has been developed. The E-CELL 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 well-mixed 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, open-source, 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...
  • Memtype-2L

  • 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...
  • iMethyl-PseAAC

  • Referenced in 21 articles [sw22443]
  • predictor, called iMethyl-PseAAC. 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 object-oriented approach...
  • LASSIE

  • Referenced in 1 article [sw29330]
  • LASSIE: simulating large-scale models of biochemical systems on GPUs. Results: LASSIE is a “black...
  • HSimulator

  • Referenced in 2 articles [sw22841]
  • multithread simulator for mass-action biochemical reaction systems placed in a well-mixed 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 cell-scale biochemical simulations. It simulates each molecule of interest individually ... they would in a real biological system. Smoldyn is easy to use and easy...