Annotation Explorer · Help ← Back to the app

Overview & quick start

Annotation Explorer ranks research papers on scRNA-seq cell annotation, summarizes each paper, and shows where it fits in the scRNA-seq analysis workflow. It supports the BSU-UB cell annotation project for Dr. Anne Talkington's group.

What's on the screen

Click a region to read about it.

Paper listEvery paper from the literature sweep, in rank order, grouped by tier. Search, filter, and pick a paper. Enhanced abstractThe agent's summary of the selected paper, plus links, citations, ranking scores and any marker definitions. Workflow panelHow the paper relates to each scRNA-seq step, or, in the "All ingested papers" view, the most-used tools and methods at each step.

The borders between these sections can be dragged to resize them (details).

Quick start

  1. Pick a paper in the list on the left. Papers marked ● ingested have been read by the agent and have full summaries; ○ pending papers show only their ranking and metadata.
  2. Read the summary at the top right: the one-line summary first, then the headed sections, and the "Why it matters for this project" note.
  3. Check the workflow panel at the bottom: dark boxes are where the paper makes its main contribution. Click a box for details.
  4. Compare across papers: switch the workflow panel to All ingested papers to see which tools and methods are used most at each step.

Running the app

From the annotation_explorer folder:

python pipeline/build_index.py
python -m http.server 8765 --directory web

Then open http://localhost:8765. The first command ranks the papers and collects the agent's summaries into the app's data file; run it again whenever papers are added. The app has to be served this way: opening index.html directly from disk won't load its data (why).

Help topics

Paper list & abstractSearching, filtering, reading a summary, links and citations. Workflow panelPer-paper workflow mapping, cross-paper tool usage, tool cards. How papers are rankedRelevance tiers from the screening rules, then recency and citations. Adding papersHow the agent reads papers and how to add more. Data sources & limitationsWhere the data comes from and what not to over-read. TroubleshootingData not loading, missing papers, odd layouts.