Paper list & abstract
The left side lists every paper in rank order; the top right shows the selected paper's enhanced abstract.
The paper list
Papers are grouped by relevance tier (Preferred Use with caution Later Out of scope) and sorted within each tier. See how papers are ranked. Each row shows:
- #rank: position in the overall ranking.
- Title, first author and year, and citation count (from OpenAlex).
- ● ingested if the agent has read the paper, or ○ pending if it hasn't yet.
Searching and filtering
- Search box: matches the title, authors, journal, category and focus, and, for ingested
papers, the names of tools they use (e.g. type
Seurat). - Tier chips: show one tier at a time; the number is how many papers are in it.
- Ingested only: hides papers the agent hasn't read yet.
- Tool filter: a chip such as Using Seurat (7) appears when you click "Show only these papers" on a tool card. Click its × to clear it.
Filters combine: for example, Preferred + Ingested only + a search term.
Keyboard
| Keys | What it does |
|---|---|
| ↑ ↓ | Select the previous or next paper in the list (when you're not typing in a box). |
| Tab, then Enter or Space | Move to a paper and select it. |
| ← → / ↑ ↓ on a focused border | Resize sections (see resizing). |
Sharing a paper
The address bar changes to …/#<paper-id> when you select a paper. Copy that address
to link someone straight to it (they need the app running too).
The enhanced abstract
For ingested papers the agent writes its own summary of the paper. It isn't a copy of the published abstract.
Tags under the title
| Tag | Meaning |
|---|---|
| Tier · #N in tier | The paper's relevance tier and its position within that tier. |
| Rule N | Which screening rule decided the tier (the rules). |
| Category · focus | The paper's area in the literature sweep, e.g. llm agent · agent. |
| recent | Published in the last 5 years. |
| defines markers | The paper gives explicit marker genes for one or more cell types. |
Summary sections
- In one line: what the paper does and its headline result.
- Headed sections: usually problem, method, evaluation and results.
- Key findings / Limitations: including limitations the authors state.
- Why it matters for this project: relevance in terms of the screening rules.
- Source line (at the bottom): what the agent read, when, and anything it couldn't read (e.g. "abstract only"). Check it before relying on a summary.
Marker definitions
If the paper defines cell types by marker genes, a table lists them: positive
markers in green, negative markers (genes that should not be expressed) in red,
and the species/tissue context. Gene symbols are kept as the paper writes them, so mouse genes appear in
mouse case (e.g. Tcf7) and surface proteins are marked (protein). These rows are
raw material for annotation rules.
Links box
Free full text (and how it's available: PMC open access, preprint, arXiv…), DOI, PubMed and OpenAlex records, then code, datasets and other links the agent found in the paper.
Citations box
Total citations from OpenAlex, citations per year, the date the count was fetched, and a bar chart of citations by year (hover a bar for the exact number). Counts are a snapshot; see limitations.
Ranking box
The paper's overall rank and the three scores used to order papers within a tier: recency, citations, and their combination. See how they're calculated.
Papers that aren't ingested yet
Instead of a summary you'll see the screening note, why the paper was listed, and the commands to ingest it (adding papers). The workflow panel has nothing to show for these papers.
Resizing the sections
- Drag the border between the paper list and the right side, between the abstract and the workflow panel, or (on wide screens, over 1200px) between the workflow diagram and the step details.
- A border highlights when you hover over it. You can also Tab to it and use the arrow keys.
- Double-click a border to reset it.
- Sizes are remembered in your browser. On narrow screens the sections stack and can't be resized.
Light and dark mode
The app and these help pages follow your system's light or dark setting.