ModeRator — Stoichiometric Model Comparison

Load Models

Model A

Choose file

Model B

Choose file

Upload & Parse

No models handy? Try two Clostridium acetobutylicum reconstructions: ClAceto1.xml and ClAceto2.xml.

{{ state.modelA.name }} {{ state.modelA.metabolites.length }} metabolites · {{ state.modelA.reactions.length }} reactions · {{ state.modelA.compartments.length }} compartments

{{ state.modelB.name }} {{ state.modelB.metabolites.length }} metabolites · {{ state.modelB.reactions.length }} reactions · {{ state.modelB.compartments.length }} compartments

Compartment Mapping

optional

Align compartment identifiers between models. Skip if they already match.

Model A compartment	Corresponds to Model B compartment
{{ comp }}

Apply

Skip

✓ Done

Metabolite Comparison

Alpha (sequence ratio weight) {{ state.metParams.alpha.toFixed(1) }}

Beta (Levenshtein weight) {{ state.metParams.beta.toFixed(1) }}

Max hydrogen difference {{ state.metParams.tolerate_h }}

Options

Ignore compartments Require exact ID match Phonetic name matching

Compare Metabolites

{{ state.metResults.length }} candidate pairs · {{ state.metResults.filter(r => r.approved).length }} approved

Approve all with Dscore ≤ {{ state.dscoreThreshold.toFixed(2) }}

Approve all

Reject all

✓	Name A	Name B	ID A	ID B	Formula A	Formula B	Dscore	ΔH
	{{ row.nameA }}	{{ row.nameB }}	{{ row.idA }}	{{ row.idB }}	{{ row.formulaA }}	{{ row.formulaB }}	{{ typeof row.dscore === 'number' ? row.dscore.toFixed(3) : row.dscore }}	{{ row.diff_h_count }}

Apply Metabolite Mapping

✓ Mapping applied

Reaction Comparison

Max substrate diff (left) {{ state.rxnParams.threshold_left }}

Max product diff (right) {{ state.rxnParams.threshold_right }}

Min metabolites for comparison {{ state.rxnParams.overall_threshold }}

Min similarity {{ state.rxnParams.similarity_threshold }}%

Compare metabolites by

Options

Cumulative threshold Only missing metabolites Allow reverse direction Require EC match Greedy (one-to-one) matching

Compare Reactions

{{ state.rxnResults.length }} matching pairs · {{ state.rxnResults.filter(r => r.approved).length }} approved (green = identical · yellow = tie · pink = non-greedy match)

✓	Name A	Name B	Reaction A	Reaction B	Sim.	EC
	{{ row.r0_name }}	{{ row.r1_name }}	{{ row.r0_id_string }}	{{ row.r1_id_string }}	{{ (row.similarity * 100).toFixed(0) }}%	{{ row.ec_result }}

Export

Metabolites CSV

Reactions CSV

Merged SBML