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Canvas and side panels

The Map Builder window with the built-in example, with callouts on the left panel tabs, the toolbar, the canvas, the inspector and the condition bar.

The Map Builder window, here with the built-in central carbon example.
  1. Left panel with three tabs: Elements, Model, Data (Alt+1/2/3).
  2. Toolbar: panels, drawing tools, undo/redo, grid and snapping, zoom, fit.
  3. Canvas.
  4. Inspector: the selected item, or the whole figure.
  5. Condition bar: conditions, animation and comparison mode.

Top bar and toolbar

The top bar holds the workspace switcher, the File menu, the editable figure name, the search / command palette (Ctrl+K) and Export.

The Map Builder toolbar: toggle left panel, Select, Pan, Metabolite, Slot, Reaction and Text tools, Undo and Redo, Show grid and Snap to grid, the zoom level, Fit all, and toggle inspector.

Tool Key Use
Select V Click to select, drag to move, drag on empty canvas to box-select.
Pan C Drag to move the view. Also: hold Space and drag, or drag with the right mouse button.
Metabolite M Click to place a metabolite node (search the model to bind it).
Slot S An empty placeholder node, bound later (see Linking a map to a model).
Reaction R Draw an arrow between nodes.
Text T Place a text label.

Then come undo / redo (Ctrl+Z / Ctrl+Shift+Z), Show grid and Snap to grid (independent of each other), the zoom level (click to reset to 100 %), Fit all (F; Shift+F fits the selection) and the inspector toggle.

The recommended way: C to move, V to work, the wheel to zoom

Press C for the hand and drag to move around the map; press V to go back to Select and work on it; zoom with the mouse wheel, which zooms around the pointer. Switching between C and V all the time is the fastest and safest way to work: with the hand, a drag never moves or selects anything by accident.

  • Zoom with the mouse wheel, + / -, or the zoom buttons. On a trackpad, pinch to zoom.
  • Pan with the hand tool (C), or hold Space and drag, or drag with the right or middle mouse button (a right-click without moving still opens the context menu). On a trackpad, move two fingers; Shift + wheel scrolls sideways.
  • F fits the whole figure, Shift+F the selection; click the zoom level to reset to 100 %.
  • The minimap in the lower right corner shows the whole figure and the visible window.

Selecting and moving

  • Click to select; Shift-click adds to the selection; drag on empty canvas to box-select. Ctrl+A selects everything.
  • Drag to move. Smart guides snap to the alignment of nearby items (turn them off in the figure settings, or hold Alt while dragging). Shift-drag constrains movement to 0°, 45° or 90°.
  • Arrow keys nudge by 1 unit, Shift + arrow by 10.
  • L locks the selection: locked items are skipped by clicks and box selection, so a background or a finished part cannot move by accident. Hold the mouse on a locked item for 3 s, or right-click it, to unlock.
  • Ctrl+C / Ctrl+V / Ctrl+D copy, paste and duplicate; Del removes; Ctrl+G groups the selection as a pathway, Ctrl+Shift+G ungroups.

A floating toolbar next to the selection offers the actions that fit it: bind a node to a model metabolite, expand one reaction upstream or downstream, add a linked plot, reverse an arrow, change its routing, find routes, collapse arrows, and, for several items, layouts and Align & distribute (see Drawing pathways).

The left panel

The Elements tab of the left panel: the six tools, the list of pathway templates with coverage badges such as 25/25 for the Global central carbon metabolism template, a link to the Template Builder, and further sections.

The Elements tab. With a model loaded, each pathway template shows its coverage of that model (for example 25/25); a ? means some matches still need review.
Tab Contents
Elements The drawing tools; pathway templates (built-in and yours, with coverage badges); Template Builder →; shapes; My templates saved from a selection; annotations: panel label, figure title, pathway label, compartment box.
Model The bound GEM with its size and validation notes; a search over IDs, names, genes, EC numbers and pathways, with buttons to add a metabolite or a reaction (with its metabolites), focus a node or expand downstream; Find metabolic path….
Data Import of flux and other data; datasets; conditions (rename, recolour, reorder, set a time); Map data → visual: mappings from datasets to arrow width, colour, opacity or label and to node radius, fill or opacity; saved views. See Displaying and comparing results.

As in the inspector, the sections of these tabs (for example Pathway templates or Shapes) fold with a click on their title, and the panel remembers which ones are folded.

The inspector

The right panel adapts to the selection. Its sections fold with a click on their title (Expand all / Collapse all at the top).

Selection What the inspector offers
Nothing Figure settings: name, style preset, global label mode for metabolites and reactions (ID / name / none), Show flux values, cofactors hidden or as inline text, legend on/off, node radius, edge width, font sizes, grid, snapping, smart guides, layout spacing.
A metabolite Model identity (Inspect in COBRAGUI →), template mapping and its candidates, formula, charge, compartment, values per condition, appearance (label, label position, radius, style, fill, lock), connected reactions with Hide zero-flux reactions, Upstream / Downstream.
A reaction Model identity and equation, participants shown on this arrow, flux in the active condition and in every condition, FVA ranges, bounds, genes, subsystem, EC, appearance (label, routing straight / curved / orthogonal, curvature, solid or dashed line, Reverse, Flip label), Routes, Linked plots.
A plot, text, group or the legend Their own properties: plot type, dataset, size; text, size, weight, colour; group title, kind, background, border, padding; legend size.
Several items Layouts, circle options, Tidy selection, Collapse into one arrow, label settings for all selected metabolites, routing for all selected reactions, + density plot for each.

Map Builder inspector for reaction PFK on the iML1515 map: equation atp_c + f6p_c → adp_c + fdp_c + h_c, participants shown f6p_c and fdp_c with three hidden cofactors, flux 6.65 mmol gDW⁻¹ h⁻¹ in the pFBA condition, bounds 0 → 1000, genes b3916 or b1723, subsystem, EC 2.7.1.11, appearance controls, routes and linked plots.

A reaction on the map (PFK): its participants, its flux in each condition and its appearance.

Map Builder inspector for the pyruvate node: template mapping with pyr_c (cytosol) mapped automatically with High confidence and pyr_e and pyr_p listed as Low-confidence alternatives because of the compartment, details, turnover per condition, appearance and the 70 connected reactions as chips marked produces or consumes.

A metabolite on the map (pyr_c): template mapping with its alternatives, data and connected reactions.

Context menu and command palette

Right-click on the canvas or on an item for the actions of that place or item: add a metabolite, slot, text or panel label here; expand the network upstream (1 or 2 steps) or downstream (1, 2 or 5 steps); bind, rebind, confirm or clear a mapping; find a path or routes; change routing, flip a label, reverse an arrow; add a linked plot; group, lock, collapse; Save as template…; duplicate, paste, delete.

Ctrl+K opens the command palette: type to find a command (create, layout, labels, style, condition, file, template, view) or an element of the model to add.

All shortcuts

Press ? in the Map Builder for the list.

Keys Action
V C M S R T Select, pan, metabolite, slot, reaction, text
Space + drag, right-drag Pan
P Add a density plot to the selected reaction(s)
Ctrl+K Command palette
Ctrl+Z / Ctrl+Shift+Z Undo / redo
Ctrl+C / Ctrl+V / Ctrl+D Copy / paste / duplicate
Ctrl+G / Ctrl+Shift+G Group as pathway / ungroup
Ctrl+A Select all
Del Delete
L Lock the selection
Arrows (+ Shift) Nudge by 1 (10) units
Shift + drag Constrain to 0°, 45°, 90°
Alt + drag Ignore smart guides
F / Shift+F Fit all / fit selection
[ / ] Previous / next condition
Ctrl+S / Ctrl+O / Ctrl+E Save project / open project / export figure
Double-click canvas Add a metabolite
Drag a node's outer ring Draw a reaction (drop on empty canvas: new slot)
Double-click a label Edit the text

Next: Drawing pathways.