Metabolic network analysis link collection

Below, I list a number of links ordered according to topics within the field of metabolic pathway and network analysis. Beware: I neither guarantee that the collection is complete nor that the links are still active.

Path finding in biological networks

Branched path finding with atom tracing using RPAIRs.
Branched path finding with atom tracing.
Prediction of small molecules' metabolic pathways based on functional group composition.
FMM - Path finding and pathway analysis in KEGG.
Rahnuma - Path finding and pathway analysis in KEGG.
Didier Croes' metabolic path finding web page.
The metabolic pathway hunter tool developped by Syed Asad Rahman. Web-based.
MetaRoute by Torsten Blum. Web-based.
Arita's atom tracing tool. Web-based.
UM-BBD metabolic pathway prediction system. Web-based.
MetaRouter. Prediction of paths in metabolic networks. Web-based.
PathComp. KEGG path finding tool. Web-based.
FASPAD. Quick detection of signaling pathways. Stand-alone tool.
BDPServer. Predicts biodegradation of chemical compounds based on an machine learning approach. Web-based.
PATHetic - Path finding in BioMeta. Project homepage.

Metabolic databases

ConsensusPathDB (integration of several databases for human)
ExPASy Biochemical pathways (interactive version of Michal's pathway wall chart)
Wiki Pathways
BN++ biochemical network database
PathCase: Pathways Database System
PathwayCommons: public biological pathway information

Metabolic pathway alignment, prediction and analysis

iMAT - web tool for constraint-based integration of transcriptomic data with metabolic networks. Web-based.
TICL - web tool for automatic interpretation of a compound list. Web-based.
MetPA - pathway enrichtment analysis
KEGG spider - pathway prediction from KEGG data and given genes. Web-based.
Pathway Assistant - metabolic modelling. Web-based.
Pathway analyst - pathway prediction. Web-based.
MetNetAligner - pathway alignment tool.
Pathway alignment tool. Web-based.
MetaPath - Metabolic network expansion. Web-based.
SEBINI: Software Environment for BIological Network Inference.
CycSim: simulating with constraint-based models of metabolism.
Tools for the efficient computation of elementary modes and extreme rays.
Tools for the Computation of Elementary Flux Patterns.
Collection of programs related to elementary mode analysis.
YANA - elementary mode analysis and extraction of metabolic networks from KEGG. Stand-alone.
DESHARKY - synthesize a query compound given the metabolic network of E. coli. Stand-alone.
bisscat - Find chemical compounds with common substructure

Metabolic comparison and reconstruction tools

Metabolic network models and model-building tools in SEED
COBRA - constraint-based reconstruction and analysis of metabolic networks
Comparative Analysis and reconstruction of metabolic networks (web-based)
Comparative Analysis of Metabolic Pathways in Metagenomics (stand-alone)
Pathway integration (web-based)
Comparative Pathway Analyser (web-based)
ComPath - Comparative Pathway Workbench (web-based)
MG-RAST - metagenome annotation, metabolic reconstruction and comparison (web-based)
SEED - genome annotation, metabolic reconstruction and comparison (web-based)
metaTIGER - comparison of metabolic profiles and phylogenomic analysis (web-based)
KEGG ortholog assignment and pathway mapping (web-based)
BioCyc Pathway tools software (stand-alone)

Metabolic pathway mapping tools

Map omics data on KEGG pathways. Web-based.
Color objects in KEGG pathways. Web-based.
KEGGanim - map high-throughput data on KEGG maps. Web-based.
Pathway tool omics viewer - map high-throughput data on BioCyc pathways. Web-based.
metaSHARK - visualization, mapping and reconstruction of metabolic pathways. Web-based.
PathExpress - Pathway mapping tool. Web-based.
PathVisio - Pathway visualization and editing. Stand-alone.
MapMan - Pathway mapping tool. Stand-alone.
GenMAPP - Pathway mapping tool. Stand-alone.
PathwayExpress - Pathway mapping tool.

Metabolic data import/export, management, visualization and editing

Publish pathway maps created with CellDesigner on the web.
Omix - Biochemical pathway visualization.
KeggConverter. Convert KGML into SBML format. Web-based or stand alone.
KGMLEdit for KEGG KGML files - Java web start.
iPath KEGG pathway browser at EMBL. Web-based.
SBMM assistant. Build metabolic models. Web-based.
MetAnnoGen - browse KEGG LIGAND. Stand-alone.
Cyclone - metabolic network construction from BioCyc. Stand-alone.
cPath. Store, visualize and analyse pathways. Stand-alone.
META-ALL - Manage metabolic pathway information.
The Chemlist dictionary to convert compound identifiers.

Graph editors, analysis and visualization tools

There is a comprehensive list of such tools in NeAT -> Information -> Links.
In addition, the following tools are of interest:
BiNoM: Cytoscape plugin, supports loading of BioPax files and some graph analysis.
VANTED: Visualization and analysis of networks with related experimental data (Java web start and stand alone)
Mavisto: network motif analysis and visualization tool (stand alone)
CentiBiN: Centralities in biological networks (Java web start and stand alone)
Heinz - find the heaviest connected subnetwork (stand-alone).


Complete Listing of All Pathguide Resources
BioPathways Consortium