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13C-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).…
CeCaFDB
Dataset

CeCaFDB Central Carbon Metabolic Flux Database

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

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…

sysmetab
Desktop

sysmetab Sysmetab

A software solving stationary and non-stationary MFA-CLE (Metabolic Flux…

A software solving stationary and non-stationary MFA-CLE (Metabolic Flux Analysis from Carbon Labeling Experiments). MFA-CLE aims to determine asymptotic reaction rates in a metabolic network from MS…

SUMOFLUX
Desktop

SUMOFLUX

A toolbox for targeted 13C metabolic flux ratio analysis. SUMOFLUX combines…

A toolbox for targeted 13C metabolic flux ratio analysis. SUMOFLUX combines surrogate modeling with machine learning and targets specific flux features individually, which makes it fast,…

MFlux
Web

MFlux

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

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…

C13
Desktop

C13

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

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,…

jQMM
Desktop

jQMM JBEI Quantitative Metabolic Modeling

Provides a method to calculate fluxes for genome-scale models. jQMM is an…

Provides a method to calculate fluxes for genome-scale models. jQMM is an open-source modular library for modelling metabolism. This library includes algorithms to measure and predict internal…

Omix
Desktop

Omix

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

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…

COBRA Toolbox
Desktop

COBRA Toolbox COnstraints Based Reconstruction and Analysis

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

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…

INCA
Desktop

INCA Isotopomer Network Compartmental Analysis

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

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…

iMS2Flux
Desktop

iMS2Flux

Automates, standardizes and connects the data flow between mass spectrometric…

Automates, standardizes and connects the data flow between mass spectrometric measurements and flux analysis programs. iMS2Flux streamlines the transfer of data from extraction via correction tools…

EMU Generator
Desktop

EMU Generator

Significantly decreases, with flux coupling, the computational burden of…

Significantly decreases, with flux coupling, the computational burden of metabolic flux analysis (MFA) when applied to large-scale metabolic models. EMU Generator was applied to a previously…

Metran
Desktop

Metran

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

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…

IsoDesign
Desktop

IsoDesign

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

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…

Iso2Flux
Desktop

Iso2Flux

Provides a software capable of 13C assisted fluxomics. Iso2Flux is an…

Provides a software capable of 13C assisted fluxomics. Iso2Flux is an application capable of integrating a wide array of experimental data (metabolites secretions and uptakes, gene expression and…

Pathway…
Desktop

Pathway Analyser

Analyzes metabolic pathways, principally by using Flux Balance Analysis (FBA)…

Analyzes metabolic pathways, principally by using Flux Balance Analysis (FBA) and Open Dynamics Engine (ODE) simulation. Pathway Analyzer performs report on gene deletions and flux values from…

iMAT
Desktop

iMAT integrative Metabolic Analysis Tool

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

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…

Metannogen
Desktop

Metannogen

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

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…

Metatool
Desktop

Metatool

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

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…

13CFLUX
Desktop

13CFLUX

A software suite of applications for the detailed quantification of…

A software suite of applications for the detailed quantification of intracellular (quasi) steady-state fluxes. 13CFLUX contains all tools for composing flexible computational (13)C-MFA workflows to…

influx_s
Desktop

influx_s

A deterministic algorithm with significantly increased numerical stability and…

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…

OpenMebius
Desktop

OpenMebius Open source software for Metabolic flux analysis

Provides the function of autogenerating metabolic models for simulating…

Provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the…

OpenFLUX
Desktop

OpenFLUX

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

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…

IsoDyn
Desktop

IsoDyn Isotopomer Dynamics

Allows users to simulate an environment for the dynamics of metabolite labeling…

Allows users to simulate an environment for the dynamics of metabolite labeling by 13C isotopes in metabolic reactions of living cells. IsoDyn is a standalone software which utilizes a classical…

WUFlux
Desktop

WUFlux

Facilitates and standardizes the 13C-metabolic flux analysis (13C-MFA) modeling…

Facilitates and standardizes the 13C-metabolic flux analysis (13C-MFA) modeling work. WUFlux is capable of directly correcting mass spectrum data of TBDMS…

KEGGconverter
Desktop
Web

KEGGconverter

It is capable of producing integrated analogues of metabolic pathways…

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…

FiatFlux
Desktop

FiatFlux

An intuitive tool for quantitative investigations of intracellular metabolism…

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…

FIA
Desktop

FIA Fluxomer Iterative Algorithm

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

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…

Biomet-toolbox
Web

Biomet-toolbox

Permits analysis of high-throughput data. Biomet-toolbox employs methods for…

Permits analysis of high-throughput data. Biomet-toolbox employs methods for flux analysis (fluxomics).

ReMatch
Desktop

ReMatch

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

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…

YANAsquare
Desktop

YANAsquare

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

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…

CLEML
Nontypeable

CLEML Carbon Labeling Experiment Markup Language

Allows representation and exchange of 13C metabolic flux analysis models. CLEML…

Allows representation and exchange of 13C metabolic flux analysis models. CLEML is a SBML dialect format.

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