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Genome-scale metabolic reconstruction

Model SEED
Web

Model SEED

A web-based resource for high-throughput generation, optimization and analysis…

A web-based resource for high-throughput generation, optimization and analysis of genome-scale metabolic models.

Pathway Tools
Desktop

Pathway Tools

Allows management, analysis, simulation and visualization of integrated…

Allows management, analysis, simulation and visualization of integrated collections of genome, pathway and regulatory data. Pathway Tools is a bioinformatics software environment around a type of…

networkRobustne…
Desktop

networkRobustnessToolbox

Allows users to estimate the structural robustness even in genome-scale…

Allows users to estimate the structural robustness even in genome-scale metabolic models (GSMMs). networkRobustnessToolbox is a rigorous and quantitative approach for the structural robustness of…

PSAMM
Desktop

PSAMM Portable System for the Analysis of Metabolic Models

Supports the iterative curation of GEnome-scale Models (GEMs) by connecting…

Supports the iterative curation of GEnome-scale Models (GEMs) by connecting model annotations with mathematical simulations. PSAMM integrates heterogeneous metadata in model annotations with the…

ReconMap
Web
Desktop

ReconMap

A comprehensive curated map of human metabolism presented utilizing the Google…

A comprehensive curated map of human metabolism presented utilizing the Google Maps application program interface (API) for highly responsive interactive navigation within a platform that facilitates…

RAVEN Toolbox
Desktop

RAVEN Toolbox Reconstruction Analysis and Visualization of Metabolic Networks

Allows users to reconstruct, analyze, simulate and visualize genome-scale…

Allows users to reconstruct, analyze, simulate and visualize genome-scale metabolic models (GEMs). The RAVEN Toolbox permits users to input GEM(s) for one or more template organisms, their…

CoReCo
Desktop

CoReCo Comparative ReConstruction

Serves for simultaneous genome-scale metabolic reconstruction of multiple…

Serves for simultaneous genome-scale metabolic reconstruction of multiple related species that leverages on the growing availability of sequenced genomes. CoReCo is a comparative metabolic…

MMD
Dataset

MMD Manchester Metabolomics Database

Allows preliminary identification of metabolites using two properties. MMD is…

Allows preliminary identification of metabolites using two properties. MMD is an online resource storing data from genome scale metabolic reconstructions, HMDB, KEGG, Lipid Maps, BioCyc and DrugBank.…

mCADRE
Desktop
AUTOGRAPH
Desktop
ElegCyc
Dataset

ElegCyc

Reflects and summarizes peculiarities of Caenorhabditis elegans metabolism…

Reflects and summarizes peculiarities of Caenorhabditis elegans metabolism distinct from most other higher eukaryotes. ElegCyc is an online resource for data integration in context of metabolism as…

Recon2Neo4j
Desktop

Recon2Neo4j

Facilitates exploration of highly-connected and comprehensive human metabolic…

Facilitates exploration of highly-connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. Recon2Neo4j provides two major components: i) a graph…

CanOE
Web

CanOE Candidate genes for Orphan Enzymes

Detects potential gap reactions. CanOe computes metabolons in a global…

Detects potential gap reactions. CanOe computes metabolons in a global metabolic network populated by reactions known to be catalyzed in the target organism. It offers a list of candidate genes for…

Pantograph
Desktop

Pantograph

Reconstructs, curates and validates genome-scale metabolic models. Pantograph…

Reconstructs, curates and validates genome-scale metabolic models. Pantograph is a template base method and a toolbox developed to help users with reconstruction model. This software exploits…

PyFBA
Desktop

PyFBA

Allows bioinformaticians to build and explore flux-balance analysis (FBA)…

Allows bioinformaticians to build and explore flux-balance analysis (FBA) models using the Python programming language. PyFBA is a python module that also permits to build models from genomes,…

GEMsplice
Desktop

GEMsplice

Allows users to link gene expression and splice isoform data to genome-scale…

Allows users to link gene expression and splice isoform data to genome-scale metabolic models. GEMsplice is a method for incorporating RNA-Seq data at the splice-isoform level into a metabolic model.…

Mackinac
Desktop

Mackinac

Combines ModelSEED’s ability to automatically reconstruct metabolic models…

Combines ModelSEED’s ability to automatically reconstruct metabolic models with COBRApy’s advanced analysis capabilities to bridge the differences between the two frameworks and to facilitate the…

SuBliMinaL…
Desktop

SuBliMinaL Toolbox

Simplifies the reconstruction process by providing a number of independent…

Simplifies the reconstruction process by providing a number of independent modules to perform common tasks. SuBliMinaL Toolbox consists of a number of independent modules that can be used…

ASBIG
Desktop

ASBIG Autocatalytic Set-Based Identification of Gaps

Detects incomplete parts of network reconstructions based on the following…

Detects incomplete parts of network reconstructions based on the following approach: identifying elements (compounds) of catalytic cycles. ASBIG recognizes inconsistencies in existing genome-scale…

L4FC
Desktop

L4FC

Provides an efficient algorithm for generic Flux Coupling Analysis (FCA). L4FC…

Provides an efficient algorithm for generic Flux Coupling Analysis (FCA). L4FC is an algorithmic framework for double and multiple knockouts in qualitative models of metabolic networks. This method…

rBioNet
Desktop

rBioNet

Implements important quality control and assurance measures (QC/QA), which are…

Implements important quality control and assurance measures (QC/QA), which are crucial for the construction of high-quality genome-scale biochemical networks. rBioNet consists of three parts: (i) a…

KEGGtranslator
Desktop
Web

KEGGtranslator

An easy-to-use stand-alone application that can visualize and convert KGML…

An easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. KEGGtranslator, unlike other translators, supports a plethora of output…

MrBac
Web

MrBac Metabolic network Reconstructions for Bacteria

Accelerates the pace of metabolic network reconstructions. MrBac streamlines…

Accelerates the pace of metabolic network reconstructions. MrBac streamlines multiple steps of draft model construction, including orthologous gene/protein identification, integration of metabolic…

FAME
Web

FAME Flux Analysis and Modeling Environment

Web-based modeling tool that combines the tasks of creating, editing, running,…

Web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program.

MicrobesFlux
Web

MicrobesFlux

A semi-automatic, web-based platform for generating and reconstructing…

A semi-automatic, web-based platform for generating and reconstructing metabolic models for annotated microorganisms.

metaSHARK
Web

metaSHARK metabolic SearcH And Reconstruction Kit

Provides an interactive visualization platform for the KEGG metabolic network…

Provides an interactive visualization platform for the KEGG metabolic network in the form of SHARKview applet. metaSHARK is useful for users that want to generate hypotheses about metabolic function…

IMGMD
Dataset

IMGMD In silico Microbial Genome-scale Metabolic Models

Provides a platform for integration and standardisation of all published…

Provides a platform for integration and standardisation of all published microbial Genome-scale metabolic models (GSMMs). IMGMD is a platform that allows users to browse, to download standardised…

MultiMetEval
Desktop

MultiMetEval Multi-Metabolic Evaluator

Analyzes large collections of metabolic models in parallel and performs…

Analyzes large collections of metabolic models in parallel and performs multi-objective analysis. MultiMetEval allows users to study secondary metabolism in actinobacteria in different ways. It…

IdentiCS
Desktop

IdentiCS Identification of Coding Sequences from Unfinished Genome Sequences

Associates the identification of coding data sequences (CDSs) with…

Associates the identification of coding data sequences (CDSs) with reconstruction, comparison and visualization of metabolic networks. IdentiCS permits users to realize reconstruction of the…

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