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📣 Announcements
Sep 18 Added ability to animate datasets with multiple time points, toggle between log and linearly scaled arrow colors, and added gene associations to reaction sidebar.
Aug 10 Apologies for the website downtime last week. I messed up the migration process between institutions. If you would like to be alerted to future issues, please follow project updates on Bluesky
▶ Quick start
1Open a pathway tab (Central Carbon, Amino Acids, or Lipid & Sterol).
2Click a reaction arrow to set custom lower/upper bounds.
3Press S or click ▶ Solve to run FBA across all maps.
Full documentation →
Preset Maps
Custom Maps
Custom Maps
No custom maps yet.
Click + to create one.
μ — h⁻¹
Connecting…
Δ diff mode
Recent Runs
No history yet.
Press Solve to record a run.
Recent Data
No datasets uploaded yet.

✦ New Map

Map name
⌕
Metabolite filter
◈
Showing reactions & metabolites involving this metabolite
Compartment filter
⬡
0 groups 0 reactions 0 metabolites selected
Groups / Subsystems
Individual Reactions
Individual Metabolites

⌀ Gene Knockouts

⌕ …
No knockouts added yet.
Search above to find a gene, reaction, or EC number
to knock out.
Gene Abundance 0 reactions mapped
Measured zero
No data for reaction
⬡ Gene Abundance
0max

Active Constraints

⌕ …
— rxn
Lower bound
Upper bound
No constraints yet.
Click any reaction arrow
in a map to add one.

⇅ Environment Editor

Drag the handles or type bounds, then apply.
⌕
Model:
Yeast-GEM ⇄ swap
Reactions:—
Metabolites:—
Solve time:—
⬤ API

Load Model

Upload an SBML (.xml) model file. The backend will regenerate
all pathway maps and re-solve. This may take a minute.

⬡
Click to browse or drag & drop an .xml file here
SBML Level 2 or 3 · COBRApy-compatible
Uploading model…

⊕ Change Objective

Build a weighted linear objective function. Search for reactions and set their weights below.

⌕ …
Weight
Objective Terms 0 terms
No reactions added yet.
Search above to add a reaction to the objective.

⚙ Settings

Appearance
Colour Scheme
✎ Editing Custom — click any swatch to edit

Load Experimental Data

Upload a CSV file with two columns: gene name/ID and abundance value.
The file will be saved and available in the experiment menu.
📂
Drag & drop a CSV file here
or click to browse
Accepted format: .csv
Uploading…

✎ Edit Model

Please choose a new model name if you would like to create a duplicate model to edit. Leaving this box blank will mean editing your current model.

✎ Edit Model

⬡ Add / Edit Metabolites 0 pending
ID
Name
Compartment
Formula
Charge
⇌ Add / Edit Reactions 0 pending
ID
Name
Lower Bound
Upper Bound
Reaction Equation — negative stoichiometry = substrate
No metabolites added yet.
◈ Add / Edit Pathways 0 pending
Name
Associated Reactions
No reactions added yet.