Table 1

Software tools developed for genome-scale metabolic reconstruction


Purpose of Tools

Implementation in the SEED

Database Contributions


The SEED already provides tools for annotation, based on similarity searching and context-based methods

The SEED already provides a database of high-quality genome annotations organized into subsystems (see [11])


Curating associations between functional roles and reactions in a particular metabolic context

Reverse-engineering of published genome-scale metabolic models; analysis of gene-reaction associations in the KEGG database; integrated display of KEGG pathway maps in subsystems, highlighting functional roles and associated reactions

Associations between functional roles and KEGG reactions in subsystems

Assembling and verifying the coherence of reaction subnetworks in subsystems

Petri net representation of KEGG reactions; encoded scenarios in subsystems; finding paths through reaction subnetworks from scenario inputs to scenario outputs

Reuseable coherent reaction subnetworks in subsystems

Assembling and verifying the coherence of connected reaction subnetworks across subsystems

Connections between scenarios in different subsystems; finding paths through connected scenarios, from overall inputs to overall outputs

List of curated subsystems with coherent reaction subnetworks for functional variants that interconnect to cover central and intermediary metabolic pathways


Assembling and verifying the coherence and completeness of an organism-specific reaction network

Identifying gaps in the reaction network, by cross-checking inputs and outputs for all paths through implemented scenarios, and checking for paths from minimal substrates to biomass compounds; creating files for FluxAnalyzer [36]

Organism-specific complete and coherent reaction networks for central and intermediary metabolism

DeJongh et al. BMC Bioinformatics 2007 8:139   doi:10.1186/1471-2105-8-139

Open Data