von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
نویسندگان
چکیده
منابع مشابه
von Bertalanffy 1.0: a 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 state mass conservation assumption and reaction directionality. Here, we introduce an algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the seco...
متن کاملStochastic von Bertalanffy models, with applications to fish recruitment.
We consider three individual-based models describing growth in stochastic environments. Stochastic differential equations (SDEs) with identical von Bertalanffy deterministic parts are formulated, with a stochastic term which decreases, remains constant, or increases with organism size, respectively. Probability density functions for hitting times are evaluated in the context of fish growth and ...
متن کاملrBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks
MOTIVATION Genome-scale metabolic networks are widely used in systems biology. However, to date no freely available tool exists that ensures quality control during the reconstruction process. RESULTS Here, we present a COBRA toolbox extension, rBioNet, enabling the construction of publication-level biochemical networks while enforcing necessary quality control measures. rBioNet has an intuiti...
متن کاملUP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction
Overexpression of key genes is a basic strategy for overproducing target products via metabolic engineering. Traditionally, identifying those key genes/pathways largely relies on the knowledge of biochemistry and bioinformatics. In this study, a modeling tool named UP Finder was developed to facilitate the rapid identification of gene overexpression strategies. It was based on the COBRA toolbox...
متن کاملElimination of thermodynamically infeasible loops in steady-state metabolic models.
The constraint-based reconstruction and analysis (COBRA) framework has been widely used to study steady-state flux solutions in genome-scale metabolic networks. One shortcoming of current COBRA methods is the possible violation of the loop law in the computed steady-state flux solutions. The loop law is analogous to Kirchhoff's second law for electric circuits, and states that at steady state t...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2010
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btq607