Saving and exporting

Projects

A project (.gemsmap) is one JSON file with everything a figure needs: the model, its template mapping profile, datasets and conditions, the drawing, the visual mappings, the view, styles and saved views. Biology/data and visuals are kept in separate parts of the file, so either can be replaced, for example a newer model under the same figure.

File menu	Shortcut
New project		An empty project: no drawing, data or model. A model returns as soon as you add something from COBRAGUI or import one.
Open example (central carbon metabolism)		The built-in example with its demonstration model and data.
Open project…	Ctrl+O	A .gemsmap file (or a .metmap file from versions ≤ 0.2). You can also drop it on the window.
Save project (.gemsmap)	Ctrl+S	Downloads the project file.
Download model as COBRA JSON		The map's model as a COBRApy-readable JSON file.

Autosave. Every 5 minutes, if something changed, the Map Builder writes the current project to a temporary session in the browser (models larger than about 2 MB go to IndexedDB). The app always opens clean and never reopens anything by itself: a welcome banner offers to continue the last session, download it as a .gemsmap file, or reopen the last COBRAGUI model — so a session that freezes the page can never lock the app. The temporary session before the current one is kept as a spare. Autosave is a safety net, not an archive: it lives in one browser profile, so save important figures as files (Ctrl S). While a template is open in the Templates workspace, the map's autosave is never overwritten.

Exporting a figure

Export (top right, or Ctrl+E) opens the export dialog.

The export dialog. The grid, the selection and handles are never exported.

Format	Use	Notes
SVG	Journals, further editing in Illustrator, Inkscape or Affinity	Vector; text stays text; dimensions in millimetres.
PDF	Vector PDF	Through the browser's print dialog: choose Save as PDF.
PNG	Slides, documents	150, 300 or 600 dpi, with the resolution stored in the file. White or transparent background.
GIF	Animated comparison of conditions	See below.

Area: the entire figure, exactly what is framed on the canvas now, or the selection. Size: Fit content, or a journal preset — single column (89 mm), 1.5 column (120 mm), double column (183 mm), full page (183 × 247 mm), A4, a 16:9 slide — or a custom width and maximum height in mm. SVG and PDF files carry these physical dimensions; PNG files carry the chosen resolution.

Animated GIF

Export → GIF plays the figure through the conditions you tick, in the order of Data → Conditions. Arrow widths, colours, node sizes and plots change from one condition to the next.

Option	Choices
Conditions	Any subset, at least two
Hold	Seconds per condition
Transition	Cut, quick, smooth or slow; smooth transitions interpolate widths, colours and node sizes
Resolution	300, 600 (default) or 900 dpi at the chosen physical size
Labels	Show the condition name on each frame
Loop	Smooth loop back to the first condition

Frames are capped at 8,000 px per side and 36 megapixels. If a large figure exported at its natural size hits the cap, the dialog says so; choose a journal width for the full resolution.

Reusing a layout

• Save as template (right-click a selection) stores the selected part of a map under Elements → My templates. Bound metabolites and reactions are turned into compartment-free hints (g6p, PFK), so the drawing re-binds to other GEMs with auto-bind.
• For reusable, identity-aware pathway templates with database identifiers, review and validation, use the Template Builder.

Next: Templates, to make a layout reusable across models.