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Search and read 8M+ biomedical papers from bioRxiv, medRxiv, and PubMed Central using the paperclip CLI.
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Draft manuscript sections, format citations, and get AI peer review. Natural language invocation -- describe what you need and the skill routes to drafting, citation formatting, or peer review. Reads research profile, data analysis outputs, and literature search results for context-aware writing. After drafting, offers to generate supporting figures via viz skills. Triggers on: "draft introduction", "write methods", "format citations", "APA style", "bibliography", "peer review", "review my draft", "write abstract". Does NOT trigger for: literature search (use sci-literature-research), data analysis (use sci-data-analysis), image generation (use viz-nano-banana), repurpose/blog/lay summary (use sci-communication).
Transfer the visual style of a reference paper figure onto the user's own data. Takes a screenshot of a figure from a paper plus tabular data and produces an editable matplotlib script in that figure's register, gated by a mechanical quality floor and a Drawer/Reviewer refinement loop. Output is a self-contained .py + PNG + Type-42 PDF. Triggers on: "match this figure style", "figure in the style of", "make my plot look like this paper", "publication figure from reference", "style transfer figure", "reproduce this figure with my data", "NeurIPS-quality version of this chart". Does NOT trigger for: plain data plots with no reference image (use sci-data-analysis), AI-generated illustrations (use viz-nano-banana), flowcharts/architecture/sequence diagrams (use viz-diagram-code), hand-drawn sketches (use viz-excalidraw-diagram).
Publish and edit markdown blog posts on Substack as drafts — converts markdown to Substack's ProseMirror schema, uploads local images to Substack's CDN, pre-renders mermaid diagrams to PNG, and creates or updates drafts via Substack's private API. Draft-only by design — publish is always a human click. Triggers on: "push to substack", "substack draft", "publish to substack", "create substack draft", "send to substack", "substack this post", "update substack", "edit substack draft", "list substack drafts". Does NOT trigger for: reading existing Substack posts, subscriber management, newsletter scheduling. Does NOT publish — only creates/updates drafts you review and publish by hand.
Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.
End-of-session checklist that reviews deliverables, collects feedback, fixes skills, updates learnings, and commits work. Use when the user says "wrap up", "close session", "end session", "wrap things up", "we're done", "that's it for today", "session done", or invokes /wrap-up. Run at the end of any working session or after completing a major deliverable. Does NOT trigger for content writing, voice extraction, positioning, or audience research.
Schedule recurring tasks that run automatically via a system-level watchdog, even when Claude Code is closed. Job definitions persist in cron/jobs/ as the registry. The watchdog (launchd on Mac, Task Scheduler on Windows) checks every hour and runs due jobs headlessly via claude -p. Triggers on: "schedule a job", "cron job", "run this every morning", "automate daily", "recurring task", "set up a scheduled job", "check scheduled jobs", "list scheduled jobs", "install watchdog", "uninstall watchdog". Does NOT trigger for one-off tasks or in-session reminders.
| name | tool-paperclip |
| description | Search and read 8M+ biomedical papers from bioRxiv, medRxiv, and PubMed Central using the paperclip CLI. |
You have access to paperclip, a CLI for searching and reading 8M+ full-text biomedical papers from bioRxiv, medRxiv, and PubMed Central (PMC).
Standalone mode: This skill works without research_context/. With a research profile it tunes query terms to the user's field; without one it runs the user's literal query. Fallback: if the paperclip CLI is not on PATH, auth is missing, or the server is unreachable, degrade gracefully to sci-literature-research (federated PubMed/arXiv/OpenAlex) and note that full-text and figure analysis are skipped until paperclip returns.
paperclip search "CRISPR delivery nanoparticle"
paperclip search "protein design" -n 50
paperclip search -s pmc "mRNA vaccine" # PMC only
paperclip search -s biorxiv "single cell" # bioRxiv only
paperclip search -e "genome-wide association study" # exact phrase
paperclip search "AlphaFold" --since 30d # recent papers
paperclip search "cancer" --journal "Cell" --year 2024 # combine filters
paperclip search "deep learning" --type review-article # article type (PMC)
paperclip search --all "protein folding" # full corpus (slower)
paperclip search --ranking vector "immune evasion" # semantic vector search only
paperclip search --ranking bm25 "TP53 R175H" # keyword BM25 only
Key options: -n/--limit, -s/--source, -e/--exact, --since, --sort [relevance|date],
--author, --journal, --year, --type, --category, -m/--mode [any|all].
paperclip grep "alphamissense" /papers/ # find term across all 8M+ papers
paperclip grep -c "BRCA[12]" /papers/ # count matches
paperclip grep "IC50.*nM" /papers/bio_4f78753a6feb/content.lines # within one paper
Runs a server-side regex engine across the full corpus in under 1 second. Use for precise text matching. For topic-based discovery, use search instead.
paperclip lookup doi 10.1101/2024.01.15.575613
paperclip lookup pmc PMC7194329
paperclip lookup pmid 32943797
paperclip lookup author "David Baker" -n 10
paperclip lookup title "CRISPR base editing"
paperclip lookup journal "Nature Medicine"
Fields: doi, author, title, abstract, source, date, pmc, pmid, publisher, type, keywords, category, license, year, volume, issue, issn.
paperclip sql "SELECT source, COUNT(*) FROM documents GROUP BY source"
paperclip sql "SELECT title, doi, source FROM documents WHERE authors ILIKE '%Doudna%' LIMIT 5"
paperclip sql "SELECT journal_title, COUNT(*) FROM documents WHERE source = 'pmc' GROUP BY journal_title ORDER BY 2 DESC LIMIT 10"
paperclip sql "SELECT title, pub_date FROM documents WHERE abstract_text ILIKE '%CRISPR%' ORDER BY pub_date DESC LIMIT 10"
Read-only SELECT on the unified documents table across all sources. Use --source pmc or --source biorxiv to filter.
Unified documents columns:
id â paper identifier (UUID for bioRxiv, PMC ID for PMC)title, doi, authors, source, abstract_text â available for all paperspub_date â publication date (text)journal_title, article_type, pmid, pub_year â PMC only (NULL for preprints)keywords (JSONB), categories (JSONB) â PMC onlyOnly the documents table is accessible. 15s timeout, 200-row limit. When id appears in results, they auto-save as a result page for use with map.
paperclip results --list # list recent result IDs
paperclip results s_4a2b61f6 # view a specific search result
paperclip results m_ec2c9cc9 # view a specific map result
Search and map commands automatically save results with IDs (e.g. s_xxx, m_xxx).
Papers live on a virtual filesystem at /papers/<id>/. Use standard UNIX commands directly:
paperclip cat /papers/<id>/meta.json
paperclip head -40 /papers/<id>/content.lines
paperclip ls /papers/<id>/sections/
paperclip grep -i "CRISPR" /papers/<id>/content.lines
paperclip scan /papers/<id>/content.lines "AAV" "efficiency" # multi-keyword search
paperclip tail -20 /papers/<id>/content.lines
paperclip awk -F, 'NR==1 || $3>100' /papers/<id>/supplements/data.csv
paperclip sed -n '10,20p' /papers/<id>/content.lines
Available commands: cat, head, tail, ls, grep, scan, sed, awk, sort, cut, tr, jq.
scan finds multiple patterns in one call â faster than repeated grep.
Important: Always use the direct syntax (paperclip cat, paperclip head, etc.) for single commands. Only use paperclip bash '...' when you need pipes or output redirection to /.gxl/:
paperclip bash 'search "CRISPR lipid nanoparticle" | grep -iE "lung|liver|in vivo"'
paperclip bash 'grep -i "IC50" /papers/<id>/content.lines | head -20'
paperclip bash 'grep -i "IC50" /papers/<id>/content.lines > /.gxl/ic50_hits.txt'
Never use paperclip bash 'cat ...' or paperclip bash 'ls ...' â use paperclip cat ... and paperclip ls ... directly.
/.gxl/Redirect output with > /.gxl/file.txt (via bash). Files persist for the session. /papers/ is read-only.
paperclip bash 'grep -i "IC50" /papers/<id>/content.lines > /.gxl/ic50_hits.txt'
paperclip bash 'awk -F, "NR==1 || $3>100" /papers/<id>/supplements/data.csv > /.gxl/filtered.csv'
paperclip ls /.gxl/
Supplementary materials live under supplements/ for many PMC papers:
paperclip ls /papers/<id>/supplements/
paperclip head -5 /papers/<id>/supplements/source_data.csv
paperclip bash 'awk -F, "NR==1 || $3>100" /papers/<id>/supplements/source_data.csv > /.gxl/filtered.csv'
# Save raw paper files to local machine with >
paperclip cat /papers/<id>/supplements/source_data.csv > source_data.csv
Append > to any paperclip command to write its output to a local file. Use >> to append.
paperclip search "CRISPR delivery" -n 10 > crispr_results.txt
paperclip cat /papers/bio_abc/meta.json > meta.json
paperclip sql "SELECT title, doi FROM documents LIMIT 20" > papers.txt
paperclip grep "deep learning" /papers/bio_abc/ > matches.txt
paperclip pull PMC10791696 # full paper -> papers/PMC10791696/
paperclip pull PMC10791696 ./my-papers/ # custom output directory
paperclip pull PMC11576387/fx1.jpg # single file -> current directory
paperclip pull bio_214f7ec77685/content.lines ./out/ # single file -> specific directory
Downloading figures/images: Binary assets download automatically when redirected:
paperclip cat /papers/bio_abc/figures/fig1.tif > fig1.tif # downloads binary
paperclip cat /papers/bio_abc/figures/fig1.tif # saves to ./fig1.tif
paperclip ask-image <id>/figures/<filename> "What does this figure show?"
paperclip ask-image <id>/figures/<filename> --fn describe # detailed description
paperclip ask-image <id>/figures/<filename> --fn extract-data # extract numbers/stats
Use paperclip ls /papers/<id>/figures/ first to see available figures.
paperclip map "What delivery methods were used?" # maps over last search results
paperclip config # show server, auth, and health status
paperclip config --url <URL> # set server URL
Each paper at /papers/<id>/:
meta.json â title, authors, doi, date, abstract, journal
content.lines â full text (line-numbered: L<n> [<block>]: <text>)
sections/ â named section files (Introduction.lines, Methods.lines, ...)
figures/ â figure files (PMC papers)
supplements/ â supplementary files (PMC papers)
Scratch space: /.gxl/ â writable, maps to CWD/.gxl/ on the user's machine.
paperclip search "your topic" to find papers. Narrow with paperclip bash 'search "broad query" | grep "must-have"'.cat on full content.lines until needed.paperclip cat /papers/<id>/meta.json then paperclip head -40 /papers/<id>/content.lines.paperclip ls /papers/<id>/sections/ then read the smallest relevant slice instead of the whole text.paperclip grep or paperclip scan for specific terms.paperclip ls /papers/<id>/figures/ then paperclip ask-image ... --fn describe.paperclip ls /papers/<id>/supplements/ then process with sed/awk via bash, or paperclip pull ... for raw files.Cite papers inline using numbered markers [1], [2], etc. At the end of your response include a REFERENCES block:
--------
REFERENCES
[1] Author A, Author B, et al. "Title of the paper." *Journal Name* vol, pages (year). doi:XX.XXXX/XXXXXXX
https://citations.gxl.ai/papers/PMC10791696#L45,L120
[2] Author C, Author D, et al. "Title of the paper." bioRxiv (year). doi:XX.XXXX/XXXXXXX
https://citations.gxl.ai/papers/bio_214f7ec77685#L210
Each reference MUST include a citations.gxl.ai link constructed from the paper's internal doc_id (the directory name under /papers/) and the L<n> line numbers where the cited claims appear:
https://citations.gxl.ai/papers/<doc_id>#L<n1>,L<n2>,...
<doc_id> is the /papers/ directory name (e.g. PMC10791696, bio_214f7ec77685).L<n> prefixes in content.lines.#L45 â range: #L45-L52 â multiple: #L45,L120,L210.meta.json.citations.gxl.ai URL is the only place where the internal doc_id appears â never expose it elsewhere in prose.head -N, section files, or grep/scan â avoid cat on the whole content.lines.sed, awk, sort, cut, tr, jq all work â use them freely for text processing.> file.txt after any command to save output locally, or > /.gxl/file.txt (via bash) to persist server-side for the session.--source pmc for peer-reviewed, --source biorxiv for preprints.-m all / -e tighten recall; combine with search | grep for precision on the shortlist.scan beats several sequential greps on the same file.for/while) and xargs are not available â use pipes or multiple tool calls.map runs an LLM reader per paper â limit inputs with -n 5 on the preceding search to keep it fast and cheap.ls /papers/<id>/figures/ then ask-image; the tool normalizes paths.