• GEPASI

  • Referenced in 34 articles [sw07916]
  • data, optimize any function of the model, perform metabolic control analysis and linear stability analysis...
  • Metatool

  • Referenced in 23 articles [sw13278]
  • powerful tool in the constraint-based modeling of metabolic networks. In recent years, new approaches...
  • SCAMP

  • Referenced in 11 articles [sw02112]
  • ANSI C compiler. SCAMP accepts metabolic models described in a biochemical language, and this enables ... simulate metabolic systems. The language is sufficiently flexible to enable other types of model ... ecological models. The language offers many facilities, including: the ability to describe metabolic pathways ... elasticities of metabolic control analysis; user-defined forcing functions at the model boundaries; user-defined...
  • BiGG

  • Referenced in 10 articles [sw17247]
  • reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature ... used to browse model content, visualize metabolic pathway maps, and export SBML files ... models for further analysis by external software packages. Users may follow links from BiGG ... have access to high quality curated metabolic models and reconstructions. It is freely available...
  • Optknock

  • Referenced in 9 articles [sw14685]
  • specified metabolite using the provided metabolic model. A nested optimization framework identifies the gene deletions...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • building integrative models of the cell that incorporate gene regulation, metabolism and signaling have ... software environment for building such integrative models based on gene sets, and running simulations ... experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic ... gene expression and other features of cellular metabolism, as a set of reaction rules...
  • BacSim

  • Referenced in 22 articles [sw17261]
  • agent simulations. The model describes bacterial properties including substrate uptake, metabolism, maintenance, cell division ... level. With the aim of making the model easily applicable to various bacteria under different...
  • Cell Illustrator

  • Referenced in 6 articles [sw06594]
  • capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways ... genomic DNA, mRNA and proteins. Cell Illustrator models are used to visualize biological pathways, interpret...
  • ScrumPy

  • Referenced in 2 articles [sw38703]
  • ScrumPy: metabolic modelling with Python. ScrumPy is a software package used for the definition ... analysis of metabolic models. It is written using the Python programming language that is also ... relevance to analysis of large (genome-scale) models. The aim is at describing ScrumPy ... readers with some knowledge of metabolic modelling, but implementation, programming and other computational details...
  • MEG

  • Referenced in 3 articles [sw10439]
  • Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. We describe ... construction of spatially distributed metabolic models, which may then be simulated using the metabolic simulator...
  • COBRA Toolbox

  • Referenced in 13 articles [sw32083]
  • widely used for modelling, analysing and predicting a variety of metabolic phenotypes using genome-scale...
  • HiPer SBTK

  • Referenced in 1 article [sw12936]
  • Simulation, characterization, and optimization of metabolic models with the high performance systems biology toolkit ... simulation and optimization components for metabolic modeling and the means to assemble these components into ... variety of different categories: model translation, model simulation, parameter sampling, sensitivity analysis, parameter estimation ... door for the systems biology metabolic modeling community to take effective advantage of large scale...
  • RelEx

  • Referenced in 7 articles [sw35376]
  • regulatory pathways, signal cascades, metabolic processes or disease models requires knowledge on individual relations like...
  • COBRApy

  • Referenced in 3 articles [sw16711]
  • widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes ... successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct ... analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software ... package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture...
  • MoNeRe

  • Referenced in 1 article [sw28180]
  • multi-omic (for instance metabolic, transcriptomic and proteomic) model. In this paper, we attempt ... first time, to combine metabolic modelling and networked Cox regression, using the metabolic model...
  • MASSpy

  • Referenced in 1 article [sw41441]
  • Python using mass action kinetics. Mathematical models of metabolic networks utilize simulation to study system ... open-source computational framework for dynamic modeling of metabolism. MASSpy utilizes mass action kinetics ... framework for constraint-based and kinetic modeling of metabolic networks. MASSpy supports high-performance dynamic ... address challenges that arise in dynamic modeling of metabolic networks, both at small and large...
  • BioMet

  • Referenced in 1 article [sw20501]
  • metabolic engineering that is driven by metabolic models. Systematic analysis of biological processes by means ... modelling and simulations has made the identification of metabolic networks and prediction of metabolic capabilities ... exploiting the capabilities of genome-scale metabolic models. The BioMet Toolbox provides an effective user ... minimized growth rates, substrate uptake rates and metabolic production rates by detecting relevant fluxes, simulate...
  • tFCA

  • Referenced in 1 article [sw17350]
  • introduced for constraint-based models of metabolic networks that are based on the steady-state ... theoretic property related to the supports of metabolic fluxes. In this paper, we further extend ... works with any kind of qualitative pathway model. We illustrate our method by thermodynamic flux ... tFCA), which allows studying steady-state metabolic models with loop-law thermodynamic constraints. These models...
  • StSNP

  • Referenced in 3 articles [sw30039]
  • mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. SNPs located within ... complex, by increasing/decreasing the activity of the metabolic pathway. Understanding the functional consequences of such ... comparative modeling of nsSNPs with links to metabolic pathway information, along with real-time visual ... modeled structures using the Friend software application. The use of metabolic pathways in StSNP allows...
  • von Bertalanffy

  • Referenced in 1 article [sw21891]
  • COBRA toolbox extension to thermodynamically constrain metabolic models. Motivation: In flux balance analysis of genome ... scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady ... reaction directionality in multi-compartmental genome scale models based on an application of the second...