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This page explains what each job type does (Main, StressME, DynamicME), what inputs you can provide, and how to interpret the outputs.

Job type Purpose When to use Key outputs
Main Single (steady-state) solve of any ME model. One condition, one solution (growth / fluxes / allocations). Fluxes, protein mass fractions, biomass composition, network data, Escher flux map (E. coli), Voronoi ProteoMap (E. coli).
StressME Single solve using the StressME E. coli model with stress parameters applied. Stress conditions (temperature, pH, ROS) for E. coli StressME. All Main outputs, but computed after stress constraints are applied.
DynamicME Time-course simulation (batch culture) using DynamicME. Media depletion / growth curves over time. Time series: biomass, growth rate (μ), external concentrations, tracked fluxes; summary plots; raw simulation JSON.
Units (important): Main/StressME exchange bounds are model flux bounds (typically mmol gDW⁻¹ h⁻¹). DynamicME initial concentrations are entered as g/L on the UI, and internally converted to mM using metabolite formula weights.

Main inputs
  • Model: upload a .pickle/.pkl ME model, or select a saved model.
  • Growth rate bounds (optional): min/max μ (h⁻¹).
  • Gene knockouts (optional): list of gene IDs.
  • Exchange bounds (optional): override LB/UB for exchanges.
  • keff overrides (optional): override reaction keff values.
  • Omics constraints (optional): upload .xlsx transcriptomics or proteomics.
  • Email (optional): receive a ZIP when the job completes.
StressME inputs
  • Model: uses the preselected StressME model (no upload required).
  • Stress Inputs: Temperature (°C), pH, ROS fold change.
  • All Main edits: growth bounds, knockouts, exchange bounds, keffs, omics, email.
DynamicME inputs
  • Model: upload a .pickle/.pkl ME model, or select a saved model.
  • Dynamic Inputs: simulation length (h), time step (h), volume (L), initial biomass (g).
  • Initial concentrations (g/L): starting concentrations for exchanges you want DynamicME to track/consume.
  • Gene knockouts / exchange bounds / keffs: supported, same UI patterns as Main.
  • Omics constraints: disabled for DynamicME on this web app (not applied in current workflow).

This Job ID is used below to demonstrate the visualization workflow.
Open in Visualize

Main / StressME
  • fluxes.csv: reaction fluxes for the solved state (often with names + stoichiometry columns).
  • mf.csv (or translation_fluxes.csv): protein allocation (mass fractions) derived from translation usage.
  • biomass_components.json: biomass contribution breakdown (interactive pie chart).
  • complex_formation.json: complex formation fluxes (interactive chart).
  • network.json: metabolite/reaction graph for network exploration.
  • flux_map.html: Escher map (E. coli only).
  • voronoi.html: Voronoi “ProteoMap” (E. coli only).
DynamicME
  • dynamicme_results.json: full time-course output (time, biomass, concentrations, tracked fluxes).
  • growth_mu.png: biomass and μ across time.
  • concentrations_mM.png / concentrations_gL.png: external concentration trajectories.
  • biomass_dilution.png: tracked biomass dilution fluxes over time.
  • translation_fluxes.png: top translation reactions over time.
Tip: The Visualize page is the canonical way to interpret results. It automatically creates interactive charts from the files in your results folder and provides download links for all outputs.