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13C-fluxomic tools

Fluxomic software tools and databases

13C-fluxomics is a new area that involves experimentally quantifying the rates of metabolic reactions within the central carbon metabolism through 13C metabolic fluxomics (Wiechert, 2001; Antoniewicz et al., 2007; Sauer, 2006; Schmidt et al., 1997). This method enables the resolution of paralleled and reversible reactions (Sauer, 2006). Source text: Zhang et al., 2014.

13CFLUX2

OMIC_06426

13CFLUX2

A software suite of applications for the detailed quantification of intracellular (quasi)…

A software suite of applications for the detailed quantification of intracellular (quasi) steady-state fluxes. 13CFLUX2 contains all tools for composing flexible computational (13)C-MFA workflows to design and evaluate carbon labeling experiments. A…

C13

OMIC_06435

C13

A tool for quantification of in vivo metabolic fluxes, from carbon labelling experiments.…

A tool for quantification of in vivo metabolic fluxes, from carbon labelling experiments. The underlying approach is metabolic flux analysis based on stationary carbon isotope labelling experiments, using fractional enrichment data.

Central Carbon Metabolic Flux Database

OMIC_06424

Central Carbon Metabolic Flux Database
CeCaFDB

A manually curated, multipurpose and open-access database for the documentation,…

A manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. CeCaFDB encompasses records for…

COnstraints Based Reconstruction and Analysis

OMIC_06004

COnstraints Based Reconstruction and Analysis
COBRA Toolbox

A software package running in the Matlab environment, which allows for quantitative…

A software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraint-based approach. Specifically, this software allows predictive computations of both steady-state and dynamic…

FiatFlux

OMIC_06429

FiatFlux

An intuitive tool for quantitative investigations of intracellular metabolism by users…

An intuitive tool for quantitative investigations of intracellular metabolism by users that are not familiar with numerical methods or isotopic tracer experiments. The aim of this open source software is to enable non-specialists to adapt the…

Fluxomer Iterative Algorithm

OMIC_06428

Fluxomer Iterative Algorithm
FIA

A powerful algorithm developed and applied to solve the MFA optimization problem. For…

A powerful algorithm developed and applied to solve the MFA optimization problem. For moderate-sized networks, the algorithm is shown to outperform the commonly used 13CFLUX cumomer-based algorithm and the more recently introduced OpenFLUX software…

influx_s

OMIC_06427

influx_s

A deterministic algorithm with significantly increased numerical stability and accuracy…

A deterministic algorithm with significantly increased numerical stability and accuracy of flux estimation compared with commonly used algorithms. It requires relatively short CPU time (from several seconds to several minutes with a standard PC…

integrative Metabolic Analysis Tool

OMIC_06448

integrative Metabolic Analysis Tool
iMAT

Enables the integration of transcriptomic and proteomic data with genome-scale metabolic…

Enables the integration of transcriptomic and proteomic data with genome-scale metabolic network models to predict enzymes’ metabolic flux. The prediction of metabolic fluxes based on high-throughput molecular data sources could help to advance…

IsoDesign

OMIC_06434

IsoDesign

Experimental design is a key step in improving both the number of fluxes that can be…

Experimental design is a key step in improving both the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values. IsoDesign that enables these parameters to be maximized by optimizing the isotopic…

Isotopomer Network Compartmental Analysis

OMIC_06432

Isotopomer Network Compartmental Analysis
INCA

A software package that can perform both steady-state metabolic flux analysis and…

A software package that can perform both steady-state metabolic flux analysis and isotopically non-stationary metabolic flux analysis. The software provides a framework for comprehensive analysis of metabolic networks using mass balances and…

KEGGconverter

OMIC_06442

KEGGconverter

It is capable of producing integrated analogues of metabolic pathways appropriate for…

It is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct…

Metannogen

OMIC_06447

Metannogen

Facilitates the reconstruction of metabolic networks. It uses the well-known database of…

Facilitates the reconstruction of metabolic networks. It uses the well-known database of biochemical reactions KEGG of biochemical reactions as primary information source from which biochemical reactions relevant to the considered network can be…

Metatool

OMIC_06450

Metatool

Elementary modes analysis is a powerful tool in the constraint-based modeling of…

Elementary modes analysis is a powerful tool in the constraint-based modeling of metabolic networks. In recent years, new approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence, the program…

Metran

OMIC_06430

Metran

A framework for the modeling of isotopic labeling systems that significantly reduces the…

A framework for the modeling of isotopic labeling systems that significantly reduces the number of system variables without any loss of information. The elementary metabolite unit (EMU) framework is based on a highly efficient decomposition method…

MFlux

OMIC_12076

MFlux

Predicts the bacterial central metabolism via machine learning, leveraging data from…

Predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms. Three machine learning methods, namely Support Vector Machine (SVM), k-Nearest Neighbors…

Omix

OMIC_06431

Omix

A software tool for the visualization of any data in biochemical networks. The unique…

A software tool for the visualization of any data in biochemical networks. The unique feature of Omix is: the software is programmable by a scripting language called Omix Visualization Language (OVL). In Omix, the visualization of data coming from…

Open source software for Metabolic flux analysis

OMIC_06433

Open source software for Metabolic flux analysis
OpenMebius

Provides the function of autogenerating metabolic models for simulating isotopic labeling…

Provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA.

OpenFLUX

OMIC_06425

OpenFLUX

A user friendly, yet flexible software application for small and large scale 13C…

A user friendly, yet flexible software application for small and large scale 13C metabolic flux analysis. The application is based on the new Elementary Metabolite Unit (EMU) framework, significantly enhancing computation speed for flux calculation.…

ReMatch

OMIC_06451

ReMatch

A web-based tool for integration of user-given stoichiometric metabolic models into a…

A web-based tool for integration of user-given stoichiometric metabolic models into a database collected from public data sources such as KEGG, MetaCyc, CheBI and ARM. ReMatch is geared particularly towards 13C metabolic flux analysis: it is…

YANAsquare

OMIC_06449

YANAsquare

Provides a software framework for rapid network assembly (flexible pathway browser with…

Provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview (visualization routine and YANAsquare editor) and network performance analysis (calculation of flux modes as…

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