Hands-on
Tutorials
Each tutorial follows one real research job from start to finish, using the commands in the order you'd actually run them. Do Get started first, because these tutorials assume you already have a library with a few papers in it.
Pick a job
Foundation
Adding papers
Four ways a PMID can surface — a citation you already have, a PICO search, a snowball, a researcher's back-catalog — plus the intake commands for URLs, PDFs, folders, bibliography files, and bare DOIs, all resolving to the one step that turns any of them into a library record.
addimportadd-urladd-pdfadd-fetchsearch-pubmedupdate-queriesrelatedpersondiscover
PhD acceptance test
Thesis chapter
Take 20 papers for one thesis question, identify what they establish, inspect disagreements, and produce a paragraph whose citations can be verified.
projectscreenattachextractverifystudycomparebriefcheck-citationsexport
Evidence synthesis
Systematic review
Save and re-run PubMed searches, record screening decisions with reasons, and freeze a PRISMA 2020 flow built from committed state.
search-pubmedupdate-queriesaddscreenfetchreviewsummarize
PI acceptance test
PI report
Confirm researcher identity, link publications to grants, and produce an annual publication report where every included paper can be traced and every unresolved match is shown.
persondiscovergrantverifypublicationsreportaudit
Reading
Papers handoff
Export a selected batch into a folder Papers.app imports from, open PDFs for reading, and pull your highlights back without touching your notes.
export-papersopenpull-annotationsnote
Discovery
Graph discovery
Weave claims into concepts and relations, find fragile and conflicting evidence, snowball from key papers, and test ABC hypotheses against PubMed.
weaveconceptrelatedgapshypothesize
How the tutorials are written
- Examples use fictional papers whose PMIDs start with
99, outside PubMed's range. That way no real paper is ever described with invented findings. - Blocks labelled output from a scratch library come from running the plugin's scripts against a throwaway library. Blocks labelled illustrative output need PubMed, the network, Papers.app, or a subagent, and follow the output format in the script source.
- Each command name links to its entry in the command reference.