Dataset Information

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.

ABSTRACT: Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

SUBMITTER: Koblitz J

PROVIDER: S-EPMC7923039 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.

Koblitz Julia J Will Sabine Eva SE Riemer S Alexander SA Ulas Thomas T Neumann-Schaal Meina M Schomburg Dietmar D

Metabolites 20210217 2

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions i ...[more]

PMID: 33671140

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Project description:BackgroundConstraint-based metabolic modeling has been applied to understand metabolism related disease mechanisms, to predict potential new drug targets and anti-metabolites, and to identify biomarkers of complex diseases. Although the state-of-art modeling toolbox, COBRA 3.0, is powerful, it requires substantial computing time conducting flux balance analysis, knockout analysis, and Markov Chain Monte Carlo (MCMC) sampling, which may limit its application in large scale genome-wide analysis.ResultsHere, we rewrote the underlying code of COBRA 3.0 using C/C++, and developed a toolbox, termed FastMM, to effectively conduct constraint-based metabolic modeling. The results showed that FastMM is 2~400 times faster than COBRA 3.0 in performing flux balance analysis and knockout analysis and returns consistent outputs. When applied to MCMC sampling, FastMM is 8 times faster than COBRA 3.0. FastMM is also faster than some efficient metabolic modeling applications, such as Cobrapy and Fast-SL. In addition, we developed a Matlab/Octave interface for fast metabolic modeling. This interface was fully compatible with COBRA 3.0, enabling users to easily perform complex applications for metabolic modeling. For example, users who do not have deep constraint-based metabolic model knowledge can just type one command in Matlab/Octave to perform personalized metabolic modeling. Users can also use the advance and multiple threading parameters for complex metabolic modeling. Thus, we provided an efficient and user-friendly solution to perform large scale genome-wide metabolic modeling. For example, FastMM can be applied to the modeling of individual cancer metabolic profiles of hundreds to thousands of samples in the Cancer Genome Atlas (TCGA).ConclusionFastMM is an efficient and user-friendly toolbox for large-scale personalized constraint-based metabolic modeling. It can serve as a complementary and invaluable improvement to the existing functionalities in COBRA 3.0. FastMM is under GPL license and can be freely available at GitHub site: https://github.com/GonghuaLi/FastMM.

Project description:Woodland caribou (Rangifer tarandus caribou) are threatened in Canada, with population and distribution declines evident in most regions of the country. Causes of declines are linked to landscape change from forest fires and human development, notably forestry oil and gas activities, which result in caribou habitat loss and affect ecosystem food webs. The Federal Species at Risk Act requires effective protection and restoration of caribou habitat, with actions to increase caribou survival. These requirements call for effective monitoring of caribou population trends to gauge success. Many woodland caribou populations are nearly impossible to count using traditional aerial survey methods, but demographic-based monitoring approaches can be used to estimate population trends based on population modeling of vital rates from marked animals. Monitoring programs have used a well-known simple population model (the Recruitment-Mortality [R/M] equation) to estimate demographic rates for woodland caribou, but have faced challenges in managing large data streams and providing transparency in the demographic estimation process. We present a stand-alone statistical software application using open-source software to permit efficient, transparent, and replicable demographic estimation for woodland caribou populations. We developed an easy-to-use, interactive web-based application for the R/M population model that uses a Bayesian estimation approach and provides the user flexibility in choice of prior distributions and other output features. We illustrate the web-application to the A la Pêche Southern Mountain (Central Group) woodland caribou population in west-central Alberta, Canada, during 1998-2017. Our estimates of population demographics are consistent with previous research on this population and highlight the utility of the application in assessing caribou population responses to species recovery actions. We provide example data, computer code, the web-based application package, and a user manual to guide installation and use. We also review underlying assumptions and challenges of population monitoring in this case study. We expect our software will contribute to efficient monitoring of woodland caribou and help in the assessment of recovery actions for this species. © 2019 The Authors. Wildlife Society Bulletin Published by Wiley Periodicals, Inc.

Dataset Information

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.

Publications

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.

Similar Datasets

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