• Matlab

  • Referenced in 12074 articles [sw00558]
  • analyze data, develop algorithms, and create models and applications. The language, tools, and built ... test and measurement, computational finance, and computational biology. More than a million engineers and scientists...
  • Bio-PEPA

  • Referenced in 102 articles [sw01361]
  • PEPA, a process algebra for the modelling and the analysis of biochemical networks ... order to handle some features of biological models, suchas stoichiometry and the use of general ... intermediate, formal, compositional representation of biological systems, on which different kindsof analysis can be carried ... show the translation of a biological model into thenew language and we report some analysis...
  • CGAL

  • Referenced in 355 articles [sw00118]
  • computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion...
  • LISREL

  • Referenced in 323 articles [sw06514]
  • modeling (SEM). SEM allows researchers in the social sciences, management sciences, behavioral sciences, biological sciences ... These theories are usually formulated as theoretical models for observed and latent (unobservable) variables...
  • DAISY

  • Referenced in 44 articles [sw09059]
  • structural property of biological and physiological models. It is considered a prerequisite for well-posed ... performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear ... biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling ... software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine...
  • BIOCHAM

  • Referenced in 40 articles [sw09927]
  • Abstract Machine (Biocham) is a modelling environment for systems biology, with some unique features ... composed of : a rule-based language for modeling biochemical systems (compatible with SBML); several simulators ... temporal properties of a biological system and validate models with respect to such specifications, unique...
  • LAMMPS

  • Referenced in 56 articles [sw05952]
  • gaseous state. It can model atomic, polymeric, biological, metallic, or granular systems using a variety...
  • VMD

  • Referenced in 83 articles [sw18651]
  • designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid...
  • CellML

  • Referenced in 25 articles [sw05635]
  • designed to facilitate the exchange of biological models across the World Wide Web. Processing applications...
  • BLAD

  • Referenced in 19 articles [sw08612]
  • Differential elimination and biological modelling. This paper describes applications of a computer algebra method, differential ... from biology. The two considered applications are related to parameter estimation and model reduction problems...
  • GenSSI

  • Referenced in 11 articles [sw10712]
  • toolbox for structural identifiability analysis of biological models. Mathematical modeling has a key role ... systems biology. Model building is often regarded as an iterative loop involving several tasks, among...
  • Reactome

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

  • Referenced in 46 articles [sw06936]
  • overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes...
  • Breach

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

  • Referenced in 8 articles [sw21957]
  • ADAM: analysis of discrete models of biological systems using computer algebra. BACKGROUND: Many biological systems ... extensive experimentation with both discrete models arising in systems biology and randomly generated networks ... biological systems, namely sparseness and robustness. For a large set of published complex discrete models ... CONCLUSIONS: Discrete modeling techniques are a useful tool for analyzing complex biological systems and there...
  • Spikenet

  • Referenced in 12 articles [sw08892]
  • networks of spiking neurons. Many biological neural network models face the problem of scalability because ... type of model one can build is not only biologically compliant, it is also computationally...
  • AIFS

  • Referenced in 14 articles [sw00023]
  • forms. The stress is put on modeling of biological forms and their atributes such...
  • Virtual Cell

  • Referenced in 8 articles [sw22589]
  • broad community of scientists. Cell biological processes are controlled by an interacting set of biochemical ... distributed within complex cellular structures. Computational modeling is familiar to researchers in fields such ... gene expression. Although some of these established modeling approaches can be adapted to address problems ... construction of cell biological models and the generation of simulations from them. The system enables...
  • ABC-SysBio

  • Referenced in 6 articles [sw24739]
  • demand for flexible tools to model and simulate biological ... systems. Two established problems in the modeling of biological processes are model selection ... designed to work with models written in Systems Biology Markup Language (SBML). Deterministic and stochastic...
  • COMBOS

  • Referenced in 8 articles [sw32081]
  • parameter combinations in nonlinear dynamic systems biology models and COMBOS: a novel web implementation...