Drawing pathways¶
There are three ways to put a pathway on the canvas, and they combine freely:
| Approach | Best for | How |
|---|---|---|
| Insert a template | Standard pathways (glycolysis, TCA, PPP…) with a recognisable layout | Elements → Pathway templates, then review the mapping and click where it goes. See Linking a map to a model and Templates. |
| Grow from the model | Exploring a neighbourhood, or drawing exactly the reactions a result highlights | Add a metabolite, then its connected reactions; expand upstream / downstream; find paths and routes; or Add to Map from COBRAGUI. |
| Draw by hand | Custom figures, schemes, or a layout before any model is loaded | Metabolites, slots, arrows and text with the tools. |
Metabolites and slots¶
- Double-click empty canvas, or use the Metabolite tool (M), to add a metabolite. With a model loaded, a search dialog binds the new node to a model metabolite.
- A slot (S, a dashed circle) is a node that is not bound yet. Slots and free arrows can be drawn before any model exists. Each slot can carry compartment-free hints (
g6p,glucose 6-phosphate) so that it binds later; see Slots and auto-bind. - Appearance (inspector): label shows the global setting, the ID, the model name or your own text; label position; radius; style normal, exchange (for boundary metabolites) or text only; fill colour; Locked.
Reactions (arrows)¶
- Drag from a node's outer ring to another node to draw an arrow. Dropping on empty canvas creates a new slot and extends the chain, so a linear pathway can be sketched in a few drags. The Reaction tool (R) does the same.
- An arrow between two bound metabolites is bound to the model reaction that links them. If no single reaction does, a series of two reactions can be shown as one lumped arrow (for example
ACONTa + ACONTb, the two half-reactions of aconitase). - An arrow drawn against the stoichiometric direction of its reaction is flagged in the inspector, and its flux sign is flipped for display. Reverse turns the arrow around.
- Participants. For reactions with many metabolites, the inspector lists which substrates and products this arrow shows; untick one to hide it from this arrow only (the model reaction is unchanged). A
+Nmarker on the canvas counts hidden participants. Cofactors are handled separately (below). - Routing: straight, curved (drag the bend handle, or set the curvature) or orthogonal; line solid or dashed (dashed is typical for exchange and transport); Flip label and Auto label position.
- If several arrows draw the same model reaction, the inspector offers Merge into one arrow.
Growing a map from the model¶
- Model tab → search: find metabolites and reactions by ID, name, gene, EC number or pathway; + adds a metabolite, or a reaction with its metabolites.
- Connected reactions. Select a metabolite: the inspector lists all its model reactions as chips, marked ↑ produces and ↓ consumes (by the written equation). Hover a chip for its name, equation, genes and bounds; click it to add the reaction. With flux data loaded, Hide zero-flux reactions keeps only reactions with flux in at least one condition.
- An added reaction brings its own copies of its other metabolites; it never silently connects itself to nodes drawn elsewhere. Extra participants start hidden. To join a copy with an existing node of the same metabolite, drag it onto that node: a green ring shows release to merge.
- Upstream / Downstream (inspector, floating toolbar or right-click) adds the reactions around a metabolite: one step from the inspector and the toolbar; 1 or 2 steps upstream and 1, 2 or 5 steps downstream from the right-click menu.
- Find metabolic path… (Model tab) draws a shortest path between two metabolites.
- Routes. Select a free arrow whose two ends are bound (for example glucose → pyruvate) and choose Find routes. The model's alternative routes are listed, shortest first. Insert draws every reaction of a route, with new copies of the intermediate metabolites; Collapsed inserts the route as one summary arrow. With flux data, Only routes that carry flux keeps routes whose every reaction carries flux in the direction the route uses it, in a chosen condition or in any condition.
- From COBRAGUI, Add to Map sends reactions, metabolites, a whole subsystem or a selection, laid out automatically. Reactions arrive as a preview that follows the mouse: click where the block goes (Esc cancels).
Currency metabolites (ATP, NAD(P)H, H₂O, H⁺, phosphate, CoA, CO₂, O₂, NH₄⁺, …) are skipped when expanding and path-finding, so paths follow carbon rather than shared cofactors. Enzyme pseudo-metabolites of enzyme-constrained models (prot_…, pmet_…) are never drawn.
Collapsing detail into one arrow¶
Select several arrows, or just two metabolites, and choose Collapse into one arrow. The sub-network is stored inside one summary arrow, and Expand restores it. The summary arrow's flux defaults to the net flux entering the segment: the sum for parallel reactions, the through-flux for a chain. Sum, mean, minimum and maximum are also available. Use this to simplify a figure without losing what is behind an arrow.
Layouts, alignment and tidying¶
With several items selected, the inspector (and the floating toolbar) offers:
| Layout | Use |
|---|---|
| Vertical / Horizontal | Linear pathways (glycolysis). |
| Circle | Cycles (TCA, urea cycle). Options: clockwise or counter-clockwise, start east, fixed diameter. |
| Hierarchical | Branching pathways, flowing in one direction. |
| Grid | Many unrelated items. |
| Organic | Force-directed arrangement of a network. |
Spacing sets the distance used by the layouts; Tidy selection straightens nearly aligned items; Align & distribute lines up edges and centres. Layouts only move what is selected.
Groups, compartments and annotations¶
- Ctrl+G groups the selection as a pathway (with a title); Group as compartment draws a compartment box. Groups move as one; Ungroup (Ctrl+Shift+G) releases them.
- Elements → Annotations adds a panel label (a, b, c…), a figure title, a pathway label or a compartment box. Text items have their own size, weight and colour; double-click to edit.
Styles¶
The figure inspector (nothing selected) sets the look of the whole figure:
- Style preset: Nature clean, Cell graphical, Minimal, Presentation, Dark, Print grayscale. Presets change appearance only, never the data.
- Labels: metabolites and reactions by ID, name or none; Show flux values next to arrows; cofactors hidden or as inline text beside their arrow.
- Sizes: node radius, edge width, font size, reaction label size.
Next: Link the map to a model, then show results on it.