• Bio-PEPA

  • Referenced in 108 articles [sw01361]
  • biochemical networks. It is a modification of PEPA, originally defined for the performanceanalysis of computer...
  • Smoldyn

  • Referenced in 23 articles [sw23962]
  • Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule...
  • Möbius

  • Referenced in 25 articles [sw04098]
  • studying the reliability, availability, and performance of computer and network systems, its use has expanded ... from biochemical reactions within genes to the effects of malicious attackers on secure computer systems...
  • SABRE

  • Referenced in 7 articles [sw12884]
  • SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization ... direct numerical approximation algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks ... also perform a deterministic analysis by directly computing a mean-field approximation of the system...
  • BioSPI

  • Referenced in 7 articles [sw11784]
  • SYSTEM FOR SIMULATION OF BIOCHEMICAL PROCESSES. BioSPI is a computer application we have developed...
  • MetaCyc

  • Referenced in 29 articles [sw08243]
  • providing a reference data set for computationally predicting the metabolic pathways of organisms from their ... genomes, supporting metabolic engineering, helping to compare biochemical networks, and serving as an encyclopedia...
  • Cellerator

  • Referenced in 8 articles [sw09926]
  • Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Summary...
  • Path2Models

  • Referenced in 4 articles [sw29332]
  • Path2Models: large-scale generation of computational models from biochemical pathway maps. Background: Systems biology projects...
  • Virtual Cell

  • Referenced in 9 articles [sw22589]
  • cell biology. The newly emerging field of computational cell biology requires software tools that address ... biochemical and electrophysiological events that are distributed within complex cellular structures. Computational modeling is familiar...
  • BALL

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

  • Referenced in 5 articles [sw35919]
  • section). For the computation of elementary flux modes (EFMs) – basic biochemical operation modes in metabolic...
  • SCAMP

  • Referenced in 11 articles [sw02112]
  • portable to all computer systems that support an ANSI C compiler. SCAMP accepts metabolic models ... described in a biochemical language, and this enables novice as well as experienced users rapidly...
  • expa

  • Referenced in 3 articles [sw35555]
  • flux maps in a biochemical reaction network, can be computed from the stoichiometric matrix...
  • sbtoolbox

  • Referenced in 18 articles [sw07391]
  • Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. We present ... analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational...
  • libSRES

  • Referenced in 2 articles [sw12828]
  • Summary: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem ... fast implementation of computer software for study of non-linear biochemical pathways. This library implements ... constraint handling technique. Considering the amount of computing time it might require to solve...
  • SPSens

  • Referenced in 1 article [sw24920]
  • package for the efficient computation of stochastic parameter sensitivities of biochemical reaction networks. Parameter sensitivity ... methods are required due to extremely high computational costs. SPSens provides efficient, state ... easily performed on stochastic models of biochemical reaction networks. SPSens implements the algorithms...
  • IGTools

  • Referenced in 3 articles [sw34225]
  • IGTools. Infogenomics Tools: A Computational Suite for Informational Analyses of Genomes. Infogenomics is a project ... biological and biochemical investigation on genomes. InfoGenomics Tools, shortly IGTools, is a computational framework, which...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed ... rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins...
  • iNA

  • Referenced in 4 articles [sw17973]
  • size expansion. The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given ... large number of existing software packages, is computationally expensive due to the huge amounts ... possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state ... which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen...
  • Hy3S

  • Referenced in 5 articles [sw23355]
  • disseminating software that simulates a chemical or biochemical system as quickly as possible, using hybrid ... other approximate algorithms to greatly reduce the computational time, but still retain accuracy...