Overview
mummichog tests patterns of candidate metabolite matches across metabolic networks, allowing functional exploration before every feature has an identification.
What can this tool do?
Common uses
- Prioritize pathways associated with differential features.
- Explore a feature table with a species-appropriate metabolic model.
Scientific fit
Primary function
Pathway and biological interpretation
Data compatibility
Inputs
Feature or peak table, Sample metadata
Outputs
Statistical results, Human-readable report
Input formats
Other, Feature table with m/z and statistical results
Output formats
Other, Pathway enrichment and network results
Scope and considerations
Designed for
- Prioritize pathways associated with differential features.
Not designed for
- Confirming individual metabolite identities or measuring metabolic flux.
Important requirements
- Feature masses, statistical results, acquisition information and a suitable metabolic model.
Considerations
- Background features and adduct assumptions affect enrichment. The current repository labels version 3 as development and retains a version 2 branch.
Access and documentation
Public source code; pin the intended release branch and consult its license.
From tool to strategy
Strategies using mummichog
Evidence and review
Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Li S, Park Y, Duraisingham S, et al. Predicting network activity from high throughput metabolomics. PLoS Comput Biol 9, e1003123 (2013). doi:10.1371/journal.pcbi.1003123
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-08 · Entry update
Audit core publications across existing tools
View change · Entry at this revision - 2026-09-07 · First committed entry
Add 50 documented metabolomics resources
View change · Entry at this revision