Papyrus keeps the whole research workflow beside the paper.

One Library

A paper should not fragment into separate tools. The PDF, metadata, reading progress, tags, notes, project role, evidence, and citation key all belong to the same object. Papyrus keeps that object coherent from first import through the final export.

The example throughout this page follows a single Nature article: A 5.3-million-year-old deep-sea whale necropolis in the Diamantina Zone. The same record appears in the library, opens in the reader, carries Markdown notes, supports a project archive, and exports through standard citation formats.

Also on iPadOS Touch-first reading, Apple Pencil, Save from Safari, iCloud sync, and the ocean-themed library. Open Close

The iPad version is presented as a companion workspace rather than a second main storyline. The demo library keeps the marine-paper set visible, so the Nature article, figure pages, Markdown notes, Pencil markup, and project context feel like one touch-first reading session.

Capture & Organize

Import should produce a usable record, not a cleanup chore. Papyrus accepts PDFs, folders on Mac, DOI and arXiv identifiers, BibTeX, and RIS. It can read embedded PDF metadata, fetch scholarly metadata, and keep field-level provenance so you can see where a title, author list, year, DOI, or abstract came from when sources disagree.

Safari can hand papers over directly. The bundled Safari extension captures the paper on the current tab — with its PDF when one is available — or saves any PDF, DOI, or arXiv link from the right-click (Mac) or long-press (iPad) menu. The popup shows exactly what was captured, says whether the PDF will download or a citation-only record will be created, and offers folder, tag, and project pickers so a paper lands organized instead of joining an inbox pile.

Organization has several layers because research changes shape over time. Tags describe topics. Folders keep stable archives. Smart Collections stay current as saved filters. Projects gather papers for a draft, review, or literature archive without forcing the global library to mirror a manuscript outline.

Read & Annotate

Reading happens in a native window, not a web viewer embedded in a database. On Mac you can highlight, underline, strike through, draw freehand ink, leave notes, and set bookmarks. The reader remembers progress and keeps annotations attached to the paper instead of scattering them into a separate notebook.³

Figure-heavy articles need more than a citation key. Papyrus lets the article page, the figure, the reading note, and the eventual claim remain adjacent. A Markdown notes pane renders headings, lists, tables, code, and LaTeX math, so a figure comment or draft-ready interpretation stays beside the source that prompted it.

Projects & Evidence

Projects turn a library into a working argument. A paper can belong to several projects, and each project can give that paper a different role. The Nature article can be an anchor source in a Diamantina whale-fall archive, while adjacent papers provide ecological context, dating methods, or organism-specific background.

The Evidence Board is the place where Papyrus goes beyond storing citations. Each evidence item records the claim you are making, the quote or observation that backs it, your interpretation, the page, the citation key, a section role, and a confidence score. A project starts to read like an argument before the manuscript exists.

Search, Sync & Privacy

A research desk has to be searchable and inspectable. Papyrus indexes titles, metadata, notes, annotations, and extracted PDF text so a phrase can lead back to the paper, page, and context where it was useful. The reading queue keeps active work visible, while filters and Smart Collections surface papers by tag, journal, year range, favorite status, document type, or PDF availability.

Local-first is the default, not an add-on. Your library, PDFs, notes, annotations, search index, and project evidence live on your device. There is no Papyrus account and no telemetry. Network access is limited to actions you choose, such as metadata lookup or sync. iCloud Sync uses your own iCloud account to keep a library current across Mac and iPad, while WebDAV sync remains available for a server destination you control and dated restore points.⁴

Export & Citation

The exit path is as important as the import path. A single paper or a whole project can leave as BibTeX, RIS, CSL JSON, Markdown, or a full bundle. Project export can include papers, notes, evidence, citations, and a report that flags missing PDFs, duplicate cite keys, sparse metadata, or unresolved citation problems before you hand work to another tool.

Citations can also be copied in common styles without leaving the library. The reference for peng2026whaleNecropolis, formatted six ways:

@article{peng2026whaleNecropolis,
  title   = {A 5.3-million-year-old deep-sea whale necropolis in the Diamantina Zone},
  author  = {Peng, Xiaotong and Zhou, Peng and Song, Xikun and Bianucci, Giovanni and others},
  journal = {Nature},
  doi     = {10.1038/s41586-026-10546-z},
  year    = {2026}
}