• Scicos

  • Referenced in 19 articles [sw01941]
  • systems, and to study physical and biological systems. New extensions allow generation of component based...
  • Breach

  • Referenced in 20 articles [sw20822]
  • complex non-linear models from systems biology...
  • LAMMPS

  • Referenced in 53 articles [sw05952]
  • model atomic, polymeric, biological, metallic, or granular systems using a variety of force fields...
  • Smoldyn

  • Referenced in 19 articles [sw23962]
  • they would in a real biological system. Smoldyn is easy to use and easy...
  • MESSI

  • Referenced in 13 articles [sw33875]
  • structure of MESSI biological systems. We introduce a general framework for biological systems, called MESSI...
  • ADAM

  • Referenced in 8 articles [sw21957]
  • ADAM: analysis of discrete models of biological systems using computer algebra. BACKGROUND: Many biological systems ... with both discrete models arising in systems biology and randomly generated networks, we found that ... with the structure maintained by most biological systems, namely sparseness and robustness. For a large ... useful tool for analyzing complex biological systems and there is a need in the biological...
  • ESPResSo

  • Referenced in 13 articles [sw06335]
  • chemistry and molecular biology. It can be used to simulate systems such ... polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes...
  • Nuc-ploc

  • Referenced in 14 articles [sw16471]
  • depth study of system biology because, in addition to helping determine their functions...
  • DESMOND

  • Referenced in 12 articles [sw06114]
  • high-speed molecular dynamics simulations of biological systems on conventional computer clusters...
  • GenSSI

  • Referenced in 11 articles [sw10712]
  • modeling has a key role in systems biology. Model building is often regarded...
  • Siconos

  • Referenced in 10 articles [sw25724]
  • Digital converter. Sliding mode control systems. Biology (Gene regulatory network). Other applications are found...
  • ABC-SysBio

  • Referenced in 6 articles [sw24739]
  • support. MOTIVATION: The growing field of systems biology has driven demand for flexible tools ... model and simulate biological systems. Two established problems in the modeling of biological processes ... parameter inference and model selection for dynamical systems in an approximate Bayesian computation (ABC) framework ... work with models written in Systems Biology Markup Language (SBML). Deterministic and stochastic models...
  • AMIGO

  • Referenced in 7 articles [sw15248]
  • toolbox for advanced model identification in systems biology using global optimization. Motivation: Mathematical models ... complex biological systems usually consist of sets of differential equations which depend on several parameters...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • BiGG addresses a need in the systems biology community to have access to high quality...
  • Bio-SPICE

  • Referenced in 9 articles [sw17246]
  • SPICE: Biological Simulation Program for Intra- and Inter-Cellular Evaluation. Bio-SPICE, an open ... source framework and software toolset for Systems Biology, is intended to assist biological researchers ... visualization tools and services to aid biological researchers engaged in building computable descriptions of cellular ... experimental validation of computational models of cell systems, our environment will offer a comprehensive substrate...
  • FisPro

  • Referenced in 9 articles [sw16651]
  • especially for simulating a physical or biological system. Fuzzy inference systems are briefly described...
  • Bio-PEPAd

  • Referenced in 5 articles [sw10690]
  • extension of Bio-PEPA. Delays in biological systems may be used to model events ... papers on the stochastic simulation of biological systems with delays. This semantics of the algebra ... deterministic framework for modeling of biological systems with delays. Finally, we prove theorems stating ... paper with an example model of biological systems with delays to illustrate the approach...
  • MEIGO

  • Referenced in 5 articles [sw08492]
  • metaheuristics for global optimization in systems biology and bioinformatics. Optimization is key to solve many ... solving diverse problems arising in systems biology and bioinformatics: enhanced scatter search method ... case studies in bioinformatics and systems biology, outperforming other state-of-the-art methods. MEIGO ... applied to multiple domains of systems biology and bioinformatics. It includes ecient state...
  • SpiCO

  • Referenced in 9 articles [sw10691]
  • modeling and simulation language for systems biology. SpiCO is based on the stochastic $pi $ calculus...
  • libSBML

  • Referenced in 9 articles [sw12937]
  • validating content expressed in the Systems Biology Markup Language (SBML) format. It is written...