Workflows by profession

A researcher's search setup

Updated 2026-07-31 · 5 min read

A research Mac is a thousand PDFs named by publisher randomness, plus data that must outlive every laptop.

The PDF library

Reference managers (Zotero, BibDesk, Papers) solve this properly — they store, rename and index the literature. If you use one fully, its search wins.

The failure mode is the *partial* library: half the PDFs managed, half as 1-s2.0-S0167...-main.pdf in Downloads. Two rules close the gap:

• Everything enters through the manager (browser connector), or
• Everything gets renamed on arrival: 2019 Smith - Mangrove economics.pdf

Zotero's stored files live under ~/Zotero/storage in hashed folders — findable by content search, not by browsing.

Searching the literature by phrase

The question is always "which paper said this":

mdfind -onlyin ~/Zotero "phrase from the paper"
mdfind -onlyin ~/Documents/Papers "tidal subsidy"

Spotlight indexes PDF text (where the PDF has a text layer — scanned older papers need OCR first), which makes it a legitimate literature-search tool aimed at your own corpus.

Datasets

Data outlives laptops or it was never data. Per project:

Project/
  data/raw/        ← never edited, ever
  data/processed/
  code/
  paper/

raw/ is append-only; processed data is reproducible from raw + code, which is what makes it safe to lose. Large raw data ages onto external drives — with the offline-search problem that implies, and the same solutions (listings, or an index that keeps offline volumes).

LaTeX

A paper is many files; name the root main.tex in a folder named for the paper, and search for the *folder*. Build artefacts (.aux, .log, .synctex.gz) are noise — .gitignore them, and a search tool that demotes rather than surfaces them earns its keep at every \include.

Common questions

How do I search inside all my papers at once?

mdfind -onlyin over your PDF folder searches full text of every paper with a text layer; OCR the scans first.

Where does Zotero keep attached PDFs?

~/Zotero/storage, one hashed subfolder per item — meant to be reached through Zotero, not browsed.