• BIOCHAM

  • Referenced in 45 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 ... properties of a biological system and validate models with respect to such specifications, unique features...
  • Bio-PEPA

  • Referenced in 105 articles [sw01361]
  • process algebra for the modelling and the analysis of biochemical networks. It is a modification ... order to handle some features of biological models, suchas stoichiometry and the use of general...
  • BioModels

  • Referenced in 32 articles [sw13610]
  • database of curated, published, quantitative kinetic models of biochemical and cellular systems. BioModels Database ... access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model...
  • GEPASI

  • Referenced in 34 articles [sw07916]
  • Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems ... biochemical reactions and provides a number of tools to fit models to data, optimize...
  • BioBayes

  • Referenced in 26 articles [sw08082]
  • uncertainty involved in the mathematical modelling of biochemical systems. There often may be a degree ... general structure of the model and about the behaviour of biochemical species which cannot ... Bayesian inference provide a consistent framework for modelling and predicting in these uncertain conditions ... estimation and evidential model ranking over models of biochemical systems defined using ordinary differential equations...
  • Celldesigner

  • Referenced in 22 articles [sw09942]
  • diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based ... Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks ... browse and modify existing SBML models with references to existing databases, simulate and view...
  • PySB

  • Referenced in 12 articles [sw13437]
  • framework for building mathematical models of biochemical systems as Python programs. PySB abstracts the complex ... equations. PySB makes it straightforward to divide models into modules and to call libraries ... macros) that encode standard biochemical actions. These features promote model transparency, reuse and accuracy. PySB...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • with which we may begin to build models for simulating intracellular molecular processes to predict ... behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized ... detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation ... RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been...
  • COPASI

  • Referenced in 70 articles [sw12253]
  • biochemical networks and their dynamics. COPASI is a stand-alone program that supports models...
  • Data2Dynamics

  • Referenced in 12 articles [sw25272]
  • this approach are to construct dynamical models of biochemical reaction networks for large datasets ... perform efficient and reliable parameter estimation for model fitting. We present a modeling environment...
  • SBML-SAT

  • Referenced in 7 articles [sw21897]
  • role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML ... known platform for coding and sharing mathematical models of such processes. However, current SBML compatible ... analysis of their SBML models of biochemical and cellular processes...
  • smfsb

  • Referenced in 6 articles [sw12260]
  • modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data...
  • COBRA Toolbox

  • Referenced in 13 articles [sw32083]
  • cellular and multicellular biochemical networks with constraint-based modelling. It implements a comprehensive collection ... modelling, analysing and predicting a variety of metabolic phenotypes using genome-scale biochemical networks...
  • SCAMP

  • Referenced in 11 articles [sw02112]
  • compiler. SCAMP accepts metabolic models described in a biochemical language, and this enables novice ... sufficiently flexible to enable other types of model to be built, e.g. chemostat or ecological...
  • Path2Models

  • Referenced in 4 articles [sw29332]
  • Path2Models: large-scale generation of computational models from biochemical pathway maps. Background: Systems biology projects ... growing number of biochemical pathway models and reconstructions. However, the majority of these models...
  • LBS

  • Referenced in 15 articles [sw12372]
  • Language for Biochemical Systems (LBS) which combines rule-based approaches to modelling with modularity...
  • BioMiner

  • Referenced in 3 articles [sw23101]
  • BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks. MOTIVATION: Understanding the biochemistry ... software system--BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based ... comprehensive, extensible and reusable data model ... BioCore--which can be used to model biochemical pathways and networks. As a first application...
  • BALL

  • Referenced in 5 articles [sw10727]
  • BALL - Biochemical Algorithms Library: Rapid Software Prototyping can significantly reduce development times in the field ... Computational Molecular Biology and Molecular Modeling. BALL (Biochemical Algorithms Library) is an application framework...
  • CANA

  • Referenced in 2 articles [sw25679]
  • models offer a simple but powerful means to understand the complex dynamics of biochemical regulation ... work we demonstrated that automata network models of biochemical regulation are highly canalizing, whereby many ... measurement of such canalization simplifies these models, making even very large networks amenable to analysis ... network dynamics, especially those used to model biochemical regulation (Gates and Rocha, 2016; Gates...
  • StochSS

  • Referenced in 6 articles [sw24921]
  • environment (IDE) for simulation of biochemical networks: Define models in an easy-to-use model...