• BIOCHAM

  • Referenced in 40 articles [sw09927]
  • Biochemical Abstract Machine (Biocham) is a modelling environment for systems biology, with some unique features ... rule-based language for modeling biochemical systems (compatible with SBML); several simulators (boolean, differential, stochastic...
  • GEPASI

  • Referenced in 32 articles [sw07916]
  • software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions...
  • BioBayes

  • Referenced in 23 articles [sw08082]
  • software package for Bayesian inference in systems biology. MOTIVATION: There are several levels of uncertainty ... involved in the mathematical modelling of biochemical systems. There often may be a degree ... model and about the behaviour of biochemical species which cannot be observed directly. The methods ... evidential model ranking over models of biochemical systems defined using ordinary differential equations. The package...
  • BioModels

  • Referenced in 29 articles [sw13610]
  • published, quantitative kinetic models of biochemical and cellular systems. BioModels Database (http://www.ebi.ac.uk/biomodels/), part ... peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated...
  • LBS

  • Referenced in 14 articles [sw12372]
  • language for biochemical systems: design and formal specification. This paper introduces a Language for Biochemical ... Systems (LBS) which combines rule-based approaches to modelling with modularity ... based on the Calculus of Biochemical Systems (CBS) which affords modular descriptions of metabolic, signalling...
  • Gromacs

  • Referenced in 113 articles [sw04128]
  • systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like ... using it for research on non-biological systems, e.g. polymers...
  • Möbius

  • Referenced in 24 articles [sw04098]
  • broad range of discrete-event systems, from biochemical reactions within genes to the effects...
  • sbtoolbox

  • Referenced in 16 articles [sw07391]
  • purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment ... analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational ... purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface ... differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large...
  • STOCKS

  • Referenced in 13 articles [sw10438]
  • STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm. STOCKS, software for the stochastic ... kinetic simulation of biochemical processes is presented. The program uses a rigorously derived Gillespie algorithm ... that the program is able to simulate systems composed of reactions varying in several orders...
  • Bio-PEPA

  • Referenced in 102 articles [sw01361]
  • modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined ... performanceanalysis of computer systems, in order to handle some features of biological models, suchas stoichiometry...
  • PySB

  • Referenced in 9 articles [sw13437]
  • framework for building mathematical models of biochemical systems as Python programs. PySB abstracts the complex ... Kappa rules and from there into systems of equations. PySB makes it straightforward to divide ... reusable elements (macros) that encode standard biochemical actions. These features promote model transparency, reuse...
  • StochKit2

  • Referenced in 8 articles [sw14081]
  • software for discrete stochastic simulation of biochemical systems with events. Summary: StochKit2 is the first...
  • BioSPI

  • Referenced in 7 articles [sw11784]
  • BioSPI SYSTEM FOR SIMULATION OF BIOCHEMICAL PROCESSES. BioSPI is a computer application we have ... developed for simulating the behavior of biochemical systems specified in the pi calculus...
  • Celldesigner

  • Referenced in 19 articles [sw09942]
  • biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed ... Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory ... with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation...
  • Hy3S

  • Referenced in 5 articles [sw23355]
  • software that simulates a chemical or biochemical system as quickly as possible, using hybrid...
  • MetMAP

  • Referenced in 3 articles [sw08672]
  • package for analysis and optimisation of metabolic systems. In previous works we have presented ... predict the parameter profile that optimizes biochemical systems regarding either a single ... model definition and a translation to S-system form and the use of widely available ... definition, analysis and optimization of a biochemical system. It starts with a given model definition...
  • SBML-SAT

  • Referenced in 6 articles [sw21897]
  • SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool. BACKGROUND ... modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become ... systems biologists a new tool for the analysis of their SBML models of biochemical...
  • Cellerator

  • Referenced in 8 articles [sw09926]
  • Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Summary ... notation to represent biochemical reactions and transcriptional activation. Multi-compartment systems are represented as graphs...
  • 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...
  • CRNreals

  • Referenced in 3 articles [sw13616]
  • used in modeling and analyzing complex biochemical systems such as metabolic networks and cell signalling...