[adamjohnwright]

@nancytli, this is the first User Guide page rewritten for the new Pathway Browser. Could you read it as a curator? The text and all of its pictures are new. Once it's merged, it'll be at beta.reactome.org/documentation/userguide/pathway-browser. Until then, the rendered text is under Files changed → the .mdx file → "Display the rich diff".

What changed

• The old page described the old browser: the Fireworks overview, GenomeSpace export, the Settings sidebar, a Key button and "+/-" expanders. It had fifteen screenshots of the old screens.
• The new text describes what the new browser does, keeping the page's structure and exercises:
  • the opening map of all pathways;
  • a numbered picture of the browser with what each numbered part does;
  • the hierarchy's icons and its Updated / New / Disease / Inferred tags;
  • the diagram Legend;
  • enhanced high-level diagrams;
  • sub-pathway shading;
  • what changes as you zoom;
  • how the hierarchy and diagram highlight each other.
• The icon table uses the browser's own icon files.

Please check these in particular

1. Exercise 3 in "Event Hierarchy Exercises" asked which reactions follow a given reaction, and pointed to the Preceding and Following Events section of the Details panel. The new browser doesn't have that section. I've changed the hint to "follow the arrows in the diagram". Is that acceptable, or should the section come back to the browser?
2. Two diagram details from the old list aren't in the new text, because I couldn't confirm how the new renderer shows them:
   • the white P box for phosphorylation;
   • the long-dashed line between overlapping sets.
     Do they still apply?
3. The pictures leave out the Feedback button, the former Pathway Browser button and the beta badge, assuming they won't be on reactome.org. Is that right?
4. Do the zoom-level description and the "Navigating Pathway Diagrams" section match what you see?

How the pictures are made

• npm run userguide:shots -- pathway-browser retakes them from beta at a fixed size in the light theme.
• After a release changes the screens, the pictures can be redone with one command.
• The other User Guide pages will follow, one PR each.

🤖 Generated with Claude Code

[adamjohnwright]

Before review: the page was fact-checked against the browser's code and corrected in the latest commit. The Expression tab shows Gene Expression Atlas data whether or not an analysis is loaded; interactor badges appear at 60% zoom rather than fading in; selecting a reaction always re-centres on it; subpathways are drawn as bands of colour along their reactions (not shaded areas); interacting pathways lie outside the pathway on screen. One more question for you, @nancytli: the Tour button plays the former browser's walkthrough video, so it shows the old screens. The page now says so. Should the video be re-recorded?

[adamjohnwright]

Correction to my question 1 above, @nancytli: the new browser does show a reaction's preceding and following events: select a reaction and its Details tab has Preceding Event and Following Events sections (e.g. R-HSA-70486 in Glucose metabolism). I had searched the wrong place and concluded it was missing. The exercise's hint and the sentence about it now point at the Details tab again, as the original did.