• Breach

  • Referenced in 26 articles [sw20822]
  • complex non-linear models from systems biology...
  • Reactome

  • Referenced in 24 articles [sw14952]
  • support basic research, genome analysis, modeling, systems biology and education. The current version...
  • Smoldyn

  • Referenced in 23 articles [sw23962]
  • they would in a real biological system. Smoldyn is easy to use and easy...
  • iLoc-Plant

  • Referenced in 18 articles [sw22419]
  • such a stringent and complicated plant protein system. As a user-friendly web-server, iLoc ... tool for Molecular Cell Biology, Proteomics, Systems Biology, and Drug Development...
  • Scicos

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

  • Referenced in 17 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...
  • REVEAL

  • Referenced in 28 articles [sw36999]
  • models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve ... depth analysis of complex dynamic systems in biology and other fields...
  • 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...
  • AMIGO

  • Referenced in 10 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...
  • Nuc-ploc

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

  • Referenced in 13 articles [sw10712]
  • modeling has a key role in systems biology. Model building is often regarded...
  • ABC-SysBio

  • Referenced in 8 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...
  • DESMOND

  • Referenced in 13 articles [sw06114]
  • high-speed molecular dynamics simulations of biological systems on conventional computer clusters...
  • libSBML

  • Referenced in 13 articles [sw12937]
  • validating content expressed in the Systems Biology Markup Language (SBML) format. It is written...
  • Siconos

  • Referenced in 12 articles [sw25724]
  • Digital converter. Sliding mode control systems. Biology (Gene regulatory network). Other applications are found...
  • Data2Dynamics

  • Referenced in 12 articles [sw25272]
  • popular approach in the field of systems biology. Two of the most critical steps ... differential equations and of the associated sensitivity system are parallelized and automatically compiled into efficient...
  • MEIGO

  • Referenced in 6 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...
  • Bio-SPICE

  • Referenced in 10 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...
  • SW1PerS

  • Referenced in 10 articles [sw17206]
  • computational biology. Biological time series may contain (multiple) unknown signal shapes of systemic relevance, imperfections ... sampling densities, and signal shapes. Results on biological data are also analyzed and compared. Results ... MLP1, PAC2 and RTT101. Conclusions: In biological systems with low noise, i.e. where periodic signals...
  • SABRE

  • Referenced in 7 articles [sw12884]
  • networks. The importance of stochasticity within biological systems has been shown repeatedly during the last ... reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these ... system under study. We illustrate the different functionalities of SABRE by means of biological case...