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Metabolic network analysis software tools | Biological pathway

PathCaseMAW
Web

PathCaseMAW PathCase Metabolomics Analysis Workbench

Provides a database-enabled framework and Web-based computational tools for…

Provides a database-enabled framework and Web-based computational tools for browsing, querying, analyzing and visualizing stored metabolic networks. PathCaseMAW is easy to work with by design, and is…

G T A T C G C T A
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,…

MetaCyc
Web

MetaCyc

A comprehensive and freely accessible database describing metabolic pathways…

A comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic…

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…

MEBS
Desktop

MEBS Multigenomic Entropy Based Score pipeline

Evaluates the importance of global biogeochemical cycles or major metabolic…

Evaluates the importance of global biogeochemical cycles or major metabolic pathways in multigenomic scale. MEBS is a computational pipeline that is composed of four steps: (i) curates the metabolic…

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…

metaTIGER
Web

metaTIGER

It has been created, using genomic information from 121 eukaryotes and 404…

It has been created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes. These enzyme sequences…

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…

iPAVS
Web

iPAVS integrated Pathway resources, Analysis and Visualization System

An integrated biological pathway database designed to support pathway discovery…

An integrated biological pathway database designed to support pathway discovery in the fields of proteomics, transcriptomics, metabolomics and systems biology. The key goal of IPAVS is to provide…

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 study…

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,…

pSSAlib
Desktop

pSSAlib partial-propensity Stochastic Simulation Algorithms library

Allows users to simulate chemical reaction-diffusion networks. pSSAlib is an…

Allows users to simulate chemical reaction-diffusion networks. pSSAlib is an open source application offering a library of multiple known partial-propensity stochastic simulation algorithms (SSAs)…

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…

HPD
Web

HPD Human Pathway Database

Developed the by integrating heterogeneous human pathway data that are either…

Developed the by integrating heterogeneous human pathway data that are either curated at the NCI Pathway Interaction Database (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web…

IPAD
Web

IPAD Integrated Pathway Analysis Database

A comprehensive database covering about 22,498 genes, 25,469 proteins, 1956…

A comprehensive database covering about 22,498 genes, 25,469 proteins, 1956 pathways, 6704 diseases, 5615 diseases, and 52 organs integrated from databases including the BioCarta, KEGG, NCI-Nature…

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…

IntPath
Web

IntPath

A pathway gene relationship database that integrates data from KEGG,…

A pathway gene relationship database that integrates data from KEGG, WikiPathways, BioCyc. Currently, the following organisms are included: Homo sapiens, Mus musculus, Saccharomyces cerevisiae and…

Pro2
Web

Pro2 Proteostasis Profiler

Permits intuitive quantitative analyses and comparative visualisation of…

Permits intuitive quantitative analyses and comparative visualisation of differential expression of complex proteostasis network (PN) alterations across large disease dataset compendia such as the…

popFBA
Desktop

popFBA

Allows exploration of the space of possible interactions between heterogeneous…

Allows exploration of the space of possible interactions between heterogeneous cell populations within a putative tumour. popFBA is an extension of flux balance analysis (FBA) able to cope with the…

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.…

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