• Matlab

  • Referenced in 11496 articles [sw00558]
  • video processing, control systems, test and measurement, computational finance, and computational biology. More than...
  • KEGG

  • Referenced in 239 articles [sw13866]
  • level functions and utilities of the biological system, such as the cell, the organism ... computer representation of the biological system, consisting of molecular building blocks of genes and proteins ... diagrams of interaction, reaction and relation networks (systems information). It also contains disease and drug ... health information) as perturbations to the biological system...
  • CGAL

  • Referenced in 335 articles [sw00118]
  • aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning...
  • Gromacs

  • Referenced in 113 articles [sw04128]
  • simulate the Newtonian equations of motion for systems with hundreds to millions of particles ... using it for research on non-biological systems, e.g. polymers...
  • Cell-PLoc

  • Referenced in 90 articles [sw09126]
  • important to molecular cell biology, proteomics, system biology and drug discovery. To provide the vast...
  • Bio-PEPA

  • Referenced in 102 articles [sw01361]
  • performanceanalysis of computer systems, in order to handle some features of biological models, suchas stoichiometry ... intermediate, formal, compositional representation of biological systems, on which different kindsof analysis can be carried ... Finally, we show the translation of a biological model into thenew language and we report...
  • VMD

  • Referenced in 81 articles [sw18651]
  • displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting ... modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies...
  • BIOCHAM

  • Referenced in 40 articles [sw09927]
  • Biocham) is a modelling environment for systems biology, with some unique features for static analysis ... rule-based language for modeling biochemical systems (compatible with SBML); several simulators (boolean, differential, stochastic ... formalize the temporal properties of a biological system and validate models with respect to such...
  • iLoc-Euk

  • Referenced in 37 articles [sw22434]
  • ignored because they usually posses some unique biological functions worthy of our special notice ... used to deal with the systems containing both singleplex and multiplex proteins. As a demonstration ... deal with such a complicated and stringent system. As a user-friendly web-server, iLoc ... tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development Also, its novel approach...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • often difficult for users to formulate the biological sequences according to their desired features ... various tasks in bioinformatics and system biology. It is anticipated that...
  • Memtype-2L

  • Referenced in 39 articles [sw16472]
  • process with other molecules in a biological system. Particularly, with the avalanche of protein sequences...
  • DAISY

  • Referenced in 41 articles [sw09059]
  • test global identifiability of biological and physiological systems. A priori global identifiability is a structural ... Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns ... equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum ... Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology...
  • BioBayes

  • Referenced in 23 articles [sw08082]
  • software package for Bayesian inference in systems biology. MOTIVATION: There are several levels of uncertainty ... involved in the mathematical modelling of biochemical systems. There often may be a degree ... Bayesian inferential methodology to problems in systems biology. RESULTS: Described herein is a software package ... evidential model ranking over models of biochemical systems defined using ordinary differential equations. The package...
  • SINTEF

  • Referenced in 32 articles [sw02984]
  • modeling, including reservoir mechanics, CO2 sequestration, biological systems, and product development of engineered media...
  • sbtoolbox

  • Referenced in 16 articles [sw07391]
  • Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. We present ... Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers ... analysis and simulation of biological and biochemical systems. Additionally it is well suited ... educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface...
  • DSTool

  • Referenced in 100 articles [sw06719]
  • bifurcation points. Dynamical systems arise in many disciplins of physics, biology and chemistry - basically always ... methods employed by the theory of dynamical systems allow to compute important properties directly without...
  • BlenX

  • Referenced in 21 articles [sw12373]
  • intended for modelling any system whose basic step of computation is an interaction between ... original development was thought for biological systems. Therefore this tutorial exemplifies BlenX features on biology...
  • Celldesigner

  • Referenced in 19 articles [sw09942]
  • Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing ... simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter...
  • Reactome

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