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Metabolic network analysis software tools | Biological pathway

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BLASTX
Web

BLASTX Translated BLAST: blastx

Searches protein database using a translated nucleotide query. BLASTX is a…

Searches protein database using a translated nucleotide query. BLASTX is a BLAST search application that compares the six-frame conceptual translation products of a nucleotide query sequence (both…

ProteinLounge
Web

ProteinLounge

Develops many interactive web-based databases and software to help the…

Develops many interactive web-based databases and software to help the life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks,…

CFPS-ME
Desktop

CFPS-ME cell-free protein synthesis driven metabolic engineering

Represents a cell-free protein synthesis driven metabolic engineering tool.…

Represents a cell-free protein synthesis driven metabolic engineering tool. CFPS-ME accelerates design-build-test (DBT) cycles for optimizing and debugging biosynthetic pathways. This tool allows…

ensembleFBA
Desktop

ensembleFBA Ensemble Flux Balance Analysis

Analyses Genome-scale metabolic network reconstructions (GENREs) and improves…

Analyses Genome-scale metabolic network reconstructions (GENREs) and improves the predictive capabilities of draft GENREs by representing many alternative network structures. ensembleFBA can predict…

MetExplore
Web

MetExplore

A web server that offers the possibility to link metabolites identified in…

A web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis…

PathPred
Web

PathPred

A web-based server to predict plausible enzyme-catalyzed reaction pathways from…

A web-based server to predict plausible enzyme-catalyzed reaction pathways from a query compound using the information of RDM patterns and chemical structure alignments of substrate-product pairs.

MetaboSignal
Desktop

MetaboSignal

Allows merging metabolic and signaling pathways reported in the Kyoto…

Allows merging metabolic and signaling pathways reported in the Kyoto Encyclopaedia of Genes and Genomes (KEGG). MetaboSignal is a network-based approach designed to navigate through topological…

MetaPathways
Desktop

MetaPathways

A modular software pipeline for integrated analysis of environmental sequence…

A modular software pipeline for integrated analysis of environmental sequence information. MetaPathways performs a series of popular analyses for taxonomic profiling and functional potential with…

MCSEnumerator
Desktop

MCSEnumerator

Allows to compute the k-smallest Minimal Cut Sets (MCSs) from a given network…

Allows to compute the k-smallest Minimal Cut Sets (MCSs) from a given network structure. MCSEnumerator facilitates the calculation of thousands of minimal intervention strategies that lead to…

PASMet
Web

PASMet Prediction Analysis and Simulation of Metabolic Reaction Networks

Predicts pathways and constructs mathematical models to systematically analyse…

Predicts pathways and constructs mathematical models to systematically analyse metabolic systems. PASMet provides four main functionalities: (i) prediction, (ii) construction, (iii) simulation and…

ReactomePA
Desktop

ReactomePA Reactome Pathway Analysis

Provides enrichment analyses, including hypergeometric test and gene set…

Provides enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be applied to the genomic coordination obtained from a sequencing experiment to…

MBTPROM
Desktop

MBTPROM Mycobacterium tuberculosis Probabilistic Regulation of Metabolism

Encapsulates a substantially expanded knowledge base of underlying metabolic…

Encapsulates a substantially expanded knowledge base of underlying metabolic and regulatory mechanisms. MTBPROM2.0 is a model that can predict metabolic consequences of transcription factor (TF)…

RxnSim
Desktop

RxnSim

Computes reaction similarity based on the molecular signatures of participating…

Computes reaction similarity based on the molecular signatures of participating molecules. RxnSim is able to compare reactions based on similarities of substrates and products in addition to their…

MMinte
Desktop

MMinte Microbial Metabolic Interactions

Allows users to explore the pairwise interactions (positive or negative) that…

Allows users to explore the pairwise interactions (positive or negative) that occur in a microbial network. From an association network and 16S rDNA sequence data, MMinte identifies corresponding…

Paintomics
Web

Paintomics

An easy-to-use bioinformatics resource that facilitates the integrated visual…

An easy-to-use bioinformatics resource that facilitates the integrated visual analysis of experiments where transcriptomics and metabolomics data have been measured on different conditions for the…

redGEM
Desktop

redGEM red GEnome-scale Metabolic networks

Constructs core metabolic models from genome scale models (GEMs). redGEM is a…

Constructs core metabolic models from genome scale models (GEMs). redGEM is a systematic model reduction framework that focuses on selected metabolic subsystems and yet retains the linkages and…

lumpGEM
Desktop

lumpGEM lump GEnome-scale Metabolic networks

Captures the minimal sized subnetworks that are capable of producing target…

Captures the minimal sized subnetworks that are capable of producing target compounds from a set of defined core metabolites. lumpGEM is a mixed-integer linear programming algorithm that can generate…

Kamneva 2016
Desktop

Kamneva 2016

Finds phylogenetic relatedness to be strongest predictor of microbial…

Finds phylogenetic relatedness to be strongest predictor of microbial co-occurrence (explains about 10% of the variance in microbial co-occurrence). Kamneva_2016 is a method that introduces two new…

GLAMM
Web

GLAMM Genome-Linked Application for Metabolic Maps

A unified web interface for visualizing metabolic networks, reconstructing…

A unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks and…

NetworkReducer
Desktop

NetworkReducer

Reduces a given large-scale metabolic network to a smaller subnetwork.…

Reduces a given large-scale metabolic network to a smaller subnetwork. NetworkReducer is able to preserve the ability of the virtual organism to grow or/and to produce certain metabolites. It is…

JigCell
Desktop

JigCell JigCell Project Homepage

Supports modelers of biochemical reaction pathways. JigCell provides a model…

Supports modelers of biochemical reaction pathways. JigCell provides a model builder, run manager, comparator, and automatic parameter estimator. It permits users to understand and explain the…

Subpathway-GM
Web
Desktop

Subpathway-GM

A powerful analytical method for the identification of biologically meaningful…

A powerful analytical method for the identification of biologically meaningful metabolic subpathways. Subpathway-GM integrates ‘interesting genes’ and ‘interesting metabolites’ related to the…

SubpathwayMiner
Desktop
Web

SubpathwayMiner

An R-based software package for flexible pathway identification.…

An R-based software package for flexible pathway identification. SubpathwayMiner facilitates sub-pathway identification of metabolic pathways by using pathway structure information. Additionally,…

plantiSMASH
Web

plantiSMASH plant antibiotics & Secondary Metabolite Analysis Shell

Automates the identification of candidate plant biosynthetic gene clusters…

Automates the identification of candidate plant biosynthetic gene clusters (BGCs), as well as their comparative genomic and transcriptomic analysis. plantiSMASH results for publicly available plant…

phraSED-ML
Desktop

phraSED-ML phra Simulation Experiment Description Markup Language

Provides a text-based way to read, summarize, and create SED-ML files.…

Provides a text-based way to read, summarize, and create SED-ML files. PhraSED-ML allows modelers to use simple text commands to encode various elements of SED-ML (models, tasks, simulations, and…

BoostGAPFILL
Desktop

BoostGAPFILL

A machine learning method for hypotheses generation in gap filling and…

A machine learning method for hypotheses generation in gap filling and metabolic model refinement. BoostGAPFILL uses metabolite patterns in the incomplete network captured using a matrix…

ReactPRED
Desktop

ReactPRED

An open source flexible and customizable tool enabling users to predict…

An open source flexible and customizable tool enabling users to predict biochemical reactions and pathways. ReactPRED allows to create customizable reaction rule set automatically from an input…

MinimalNetwork
Desktop

MinimalNetwork

Allows computing minimum subnetworks. MinimalNetwork provides a Mixed integer…

Allows computing minimum subnetworks. MinimalNetwork provides a Mixed integer linear program (MILP) approach to compute for a given large metabolic network one or more minimum subnetworks preserving…

NetCooperate
Desktop
Web

NetCooperate

A package for determining host-microbe and microbe-microbe cooperative…

A package for determining host-microbe and microbe-microbe cooperative potential. NetCooperate specifically calculates two previously developed and validated metrics for species interaction: the…

GEPASI
Desktop

GEPASI GEneral PAthway Simulator

Allows users to model dynamics, steady states and control of biochemical or…

Allows users to model dynamics, steady states and control of biochemical or other systems. GEPASI has a modular structure that makes possible the existence of several user interfaces, the numerical…

MonaLisa
Desktop

MonaLisa

Provides functional analysis without prior knowledge of detailed kinetic data.…

Provides functional analysis without prior knowledge of detailed kinetic data. MonaLisa is based on the Petri net (PN) formalism and focuses on decomposition methods to identify functional modules at…

iPath
Web

iPath interactive Pathways Explorer

A web-based tool for the visualization and analysis of cellular pathways. Its…

A web-based tool for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems as annotated to date. Nodes in the map correspond to various…

MADE
Desktop

MADE Metabolic Adjustment by Differential Expression

Uses the statistical significance of changes in gene or protein expression to…

Uses the statistical significance of changes in gene or protein expression to create a functional metabolic model that most accurately recapitulates the expression dynamics. MADE is a method for…

XeDetect
Desktop

XeDetect

Analyzes the biodegradational potential of different bacterial communities…

Analyzes the biodegradational potential of different bacterial communities (BCs). XeDetect represents a powerful tool for the analysis of the metabolic capacity of BCs. It considers a community of…

Reaction…
Web
Desktop

Reaction Balance

Allows calculation of chemical reaction stoichiometries. Reaction Balance can…

Allows calculation of chemical reaction stoichiometries. Reaction Balance can pose an automatic reaction balancing as a mixed integer linear programming (MILP) and is able to define constraints…

PySCeSToolbox
Desktop

PySCeSToolbox Python Simulator for Cellular Systems Toolbox

Builds upon metabolic control analysis (MCA). PySCeSToolbox is designed to make…

Builds upon metabolic control analysis (MCA). PySCeSToolbox is designed to make use of the Jupyter Notebook as a platform for performing analyses and experiments. It combines modern computational…

MetExploreViz
Web

MetExploreViz

Allows visualization of metabolic pathways and cellular compartments of a…

Allows visualization of metabolic pathways and cellular compartments of a metabolic network by using convex hulls. MetExploreViz permits users to manually edit the representation and then save the…

SteadyCom
Desktop

SteadyCom

Infers time-averaged steady-state flux distributions in microbial communities.…

Infers time-averaged steady-state flux distributions in microbial communities. SteadyCom is a computational modeling framework which allows to predict community compositions, for stable microbial…

Pyabolism
Desktop

Pyabolism

Offers an implementation of Gene Complex (GC)-Flux algorithm. Pyabolism is a…

Offers an implementation of Gene Complex (GC)-Flux algorithm. Pyabolism is a Python module containing an algorithm that opens up the possibility of tuning expression-derived constraints individually.…

Correlation…
Desktop

Correlation Calculator

Estimates partial correlation networks. The Correlation Calculator program…

Estimates partial correlation networks. The Correlation Calculator program implements the Debiased Sparse Partial Correlation algorithm (DSPC). It is a standalone Java application providing various…

JMassBalance
Desktop

JMassBalance

Determines the salient structural properties of metabolic networks and to…

Determines the salient structural properties of metabolic networks and to identify new properties, which are statistically significant and independent of basic physical constraints. JMassBalance is a…

MetaMapR
Desktop
Web

MetaMapR

Integrates enzymatic transformations with metabolite structural similarity,…

Integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks. This open source,…

tEFMA
Desktop

tEFMA

Uses the cellular metabolome to avoid the enumeration of thermodynamically…

Uses the cellular metabolome to avoid the enumeration of thermodynamically infeasible elementary flux modes (EFMs). Specifically, given a metabolic network and a not necessarily complete metabolome,…

GNAT
Desktop

GNAT Glycosylation Network Analysis Toolbox

A platform-independent, user-extensible MATLAB-based toolbox that provides an…

A platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables…

MetNetMaker
Desktop

MetNetMaker

Allows creation and manipulation of SBML format metabolic networks with…

Allows creation and manipulation of SBML format metabolic networks with reactions and compounds defined as in the KEGG LIGAND database. MetNetMaker is an application that uses the KEGG LIGAND…

FCF
Desktop

FCF Flux Coupling Finder

Elucidates the topological and flux connectivity features of genome-scale…

Elucidates the topological and flux connectivity features of genome-scale metabolic networks and enables the global identification of blocked reactions, equivalent knockouts, and sets of affected…

OptCom
Desktop

OptCom

Provides a comprehensive flux balance analysis framework for microbial…

Provides a comprehensive flux balance analysis framework for microbial communities. OptCom relies on a multi-level and multi-objective optimization formulation to properly describe trade-offs between…

NICELips
Algorithm

NICELips Network Integrated Computational Explorer for Lipidomics

Generates associations between Kyoto Encyclopedia of Genes and Genomes (KEGG)…

Generates associations between Kyoto Encyclopedia of Genes and Genomes (KEGG) and LIPID MAPS structure Database (LMSD) databases. NICELips consists of several components integrated into a workflow…

EvoMS
Web
Desktop

EvoMS Evolutionary Metabolic Synthesizer

Represents an evolutionary algorithm for searching branched metabolic pathways…

Represents an evolutionary algorithm for searching branched metabolic pathways among a set of compounds. EvoMS performs the search taking into account the availability of substrates for each reaction…

ScrumPy
Desktop

ScrumPy

Provides a flexible package of metabolic modelling tools that experience shows…

Provides a flexible package of metabolic modelling tools that experience shows to be usable by neophyte modelers and experienced programmers. ScrumPy is useful to study metabolic models, and more…

Cell++
Desktop

Cell++

Provides the user with the flexibility to model a variety of biochemical…

Provides the user with the flexibility to model a variety of biochemical pathways from signal transduction to metabolism. Cell++ is a stochastic simulation environment with the capacity to study a…

FindPath
Desktop

FindPath

An unified system predicting and ranking the possible pathways according to…

An unified system predicting and ranking the possible pathways according to their metabolic efficiency in cellular context.

CARMEN
Web
Desktop

CARMEN Comparative Analysis and Reconstruction of MEtabolic Networks

Automates reconstruction of metabolic networks. CARMEN uses metabolic network…

Automates reconstruction of metabolic networks. CARMEN uses metabolic network analysis to facilitate a first approximation of fluxes in a metabolic network on the basis of reaction stoichiometry. It…

quasi-steady…
Desktop

quasi-steady state Petri nets

Reproduces experimentally determined qualitative dynamic behaviours and permits…

Reproduces experimentally determined qualitative dynamic behaviours and permits mechanistic analysis of genotype–phenotype relationships. QSSPN is a method integrating Petri nets and…

Pathway Flow
Web

Pathway Flow

Interprets omics lists in the context of metabolic pathway and regulatory…

Interprets omics lists in the context of metabolic pathway and regulatory networks using a statistical model for flow within the networks. Pathway Flow allows to visualized statistical results for…

SED-ED
Desktop

SED-ED

Uses to view, edit, validate and annotate the simulation experiment description…

Uses to view, edit, validate and annotate the simulation experiment description markup language (SED-ML) documents while shielding end-users from the underlying XML representation. SED-ED supports…

NetCmpt
Desktop
Web

NetCmpt

A tool for calculating the competitive potential between pairs of bacterial…

A tool for calculating the competitive potential between pairs of bacterial species. The score describes the effective metabolic overlap (EMO) between two species, derived from analyzing the topology…

NetSeed
Web

NetSeed

A web tool for analyzing the topology of metabolic networks and calculating the…

A web tool for analyzing the topology of metabolic networks and calculating the set of exogenously acquired compounds. NetSeed is based on the seed detection algorithm, that allows for the…

SBMLToolbox
Desktop

SBMLToolbox

A toolbox that facilitates importing and exporting models represented in the…

A toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an…

SED-ML
Desktop

SED-ML Simulation Experiment Description Markup Language

An XML-based format for encoding simulation setups, to ensure exchangeability…

An XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. SED-ML follows the requirements defined in the MIASE guidelines.

Pybrn
Desktop

Pybrn Biochemical network analysis with Python

Analyzes biochemical reaction networks. pybrn compiled researchers’ model…

Analyzes biochemical reaction networks. pybrn compiled researchers’ model analysis routines. Users can create basic model, handle data and evaluate them. The software is also able to analyze…

PathwayLab
Desktop

PathwayLab

Detects the causes of disorders and potential drug targets. PathwayLab allows…

Detects the causes of disorders and potential drug targets. PathwayLab allows users to modelize, analyze, and manage information from biochemical pathways. It contains a large scale of graphical…

MetaCore
Web

MetaCore

Accelerates discovery research with systems biology content, analytics, and…

Accelerates discovery research with systems biology content, analytics, and expertise. MetaCore is an integrated software suite for functional analysis of Next Generation Sequencing (NGS), gene…

UM-PPS
Web

UM-PPS University of Minnesota pathway prediction system

Recognizes functional groups in organic compounds that are potential targets of…

Recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions. UM-PPS predicts transformations of functional groups based on biotransformation rules.…

GAM
Web

GAM Genes And Metabolites

Facilitates an analysis of the metabolomic and transcriptional profiling data…

Facilitates an analysis of the metabolomic and transcriptional profiling data in the context of cellular reaction network. GAM service provides a way for a quick interactive analysis of the data to…

Metaboflux
Desktop

Metaboflux

Provides a model for helping research about system’s structure and…

Provides a model for helping research about system’s structure and semi-quantitative behavior by using structural pathway and metabolic flux analysis. Metaboflux allows users to exploit a wide…

PathExpress
Web

PathExpress

Interprets gene-expression data and explores the metabolic network without…

Interprets gene-expression data and explores the metabolic network without being restricted to predefined pathways. A graphical pathway representation permits the visualization of the expressed genes…

WIT
Dataset

WIT What Is There

Supports comparative analysis of sequenced genomes and to generate metabolic…

Supports comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal sequences and metabolic modules from the EMP/MPW family of databases. WIT contains…

PUMA2
Web

PUMA2

An interactive, integrated bioinformatics environment for high-throughput…

An interactive, integrated bioinformatics environment for high-throughput genetic sequence analysis and metabolic reconstructions from sequence data. PUMA2 provides a framework for comparative and…

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