• Virtual Cell

  • Referenced in 9 articles [sw22589]
  • modeling is familiar to researchers in fields such as molecular structure, neurobiology and metabolic pathway ... gene expression. Although some of these established modeling approaches can be adapted to address problems...
  • MetNet

  • Referenced in 2 articles [sw25662]
  • biologist to visualize, statistically analyse and model a metabolic and regulatory network map of Arabidopsis ... database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination ... develop and evaluate hypotheses, and provide a modelling framework for assessing the large amounts ... Users can highlight different parts of the metabolic network and see the relevant expression data...
  • MetNetAligner

  • Referenced in 2 articles [sw25791]
  • data allows for increasingly accurate modeling and reconstruction of metabolic networks. Alignment of the reconstructed ... networks can help to catch model inconsistencies and infer missing elements. In this note ... service tool MetNetAligner which aligns metabolic networks, taking in account the similarity of network topology...
  • Simpathica

  • Referenced in 2 articles [sw40168]
  • allows biologists to construct and simulate models of metabolic, regulatory, and signaling networks and then...
  • EPE

  • Referenced in 4 articles [sw09287]
  • energy metabolism of whole organelles, construct a kinetic model, and predict the response...
  • MetaboTools

  • Referenced in 0 articles [sw15375]
  • toolbox for analysis of genome-scale metabolic models. Metabolomic data sets provide a direct read ... data in the context of the metabolic model using constraint-based modeling. Through this work ... methods for the computational analysis of metabolic models and stratification thereof into different phenotypes ... analysis tools can be applied to metabolic models without performing the entire workflow. Taken together...
  • LBS

  • Referenced in 15 articles [sw12372]
  • which combines rule-based approaches to modelling with modularity. It is based on the Calculus ... Systems (CBS) which affords modular descriptions of metabolic, signalling and regulatory networks in terms...
  • MetaModel

  • Referenced in 4 articles [sw09011]
  • MetaModel: a program for modelling and control analysis of metabolic pathways...
  • 13cflux2

  • Referenced in 3 articles [sw11825]
  • Metabolic fluxes are the final endpoint of all co-operating actions in the complex cellular ... mathematical models. 13C-based metabolic flux analysis emerged as the state-of-the-art technique...
  • METRADE

  • Referenced in 1 article [sw28181]
  • environmental adaptability in multi-omic network models. Bacterial phenotypic traits and lifestyles in response ... multi-omic model of Escherichia coli that accounts for metabolism, gene expression and codon usage ... model, we propose a multiobjective optimization algorithm to find the allowable and optimal metabolic phenotypes ... different experimental conditions, models and bacterial strains according to their metabolic response in a multidimensional...
  • multistatepdscontrol

  • Referenced in 2 articles [sw31987]
  • cancerous growth and to a model linking intracellular iron metabolism and oncogenic pathways. The control...
  • CRNreals

  • Referenced in 5 articles [sw13616]
  • widely used in modeling and analyzing complex biochemical systems such as metabolic networks and cell ... known that the reliable inference of CRN models generally requires thorough identifiability and distinguishability analysis...
  • Psim

  • Referenced in 4 articles [sw27719]
  • computational platform for metabolic P systems. Although born as unconventional models of computation, P systems ... Nevertheless, the employment of P systems for modeling purposes demands biologically meaningful evolution strategies ... strategy of evolution known as the metabolic algorithm has been presented; here a simulation tool...
  • BMC

  • Referenced in 1 article [sw39888]
  • method to a large-scale metabolic network model of Helicobacter pylori encompassing 485 species...
  • BoostGAPFILL

  • Referenced in 0 articles [sw34262]
  • hypotheses generation in gap filling and metabolic model refinement. BoostGAPFILL uses metabolite patterns ... reactions used to fill gaps in a metabolic network. We formulate a testing framework based...
  • BacArena

  • Referenced in 0 articles [sw15883]
  • represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological...
  • RbioRXN

  • Referenced in 0 articles [sw15423]
  • integrated metabolic network and genome-scale metabolic model...
  • SBML-PET

  • Referenced in 2 articles [sw12829]
  • estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML...
  • Charlie

  • Referenced in 4 articles [sw12881]
  • model validation of natural systems, i.e. biochemical networks, such as metabolic, signal transduction, and gene...