Fluxomic software tools and databases
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…
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.
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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.
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.…
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…
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…
