Research & Citations (Zotero, JabRef)

Most students pay for software they don't need. Zotero is free, open source, syncs to your phone, integrates with Word / Google Docs / LibreOffice, and beats Mendeley on every dimension that matters. Pair with a team wiki for shared notes.

Reference managers (FOSS)

• ★ ★ Zotero — AGPL; the default. Word + Google Docs + LibreOffice plugins; browser connector saves anything; Group Libraries for collaboration; free 300 MB sync (storage upgrade is paid; use WebDAV or your own Nextcloud for free unlimited sync).
  • https://github.com/zotero/zotero
• ★ JabRef — MIT; BibTeX / BibLaTeX-flavoured; the LaTeX user's default. Java; cross-platform.
  • https://github.com/JabRef/jabref
• Bibdesk (macOS) — BSD; Mac-native BibTeX manager.
• Citavi — paid; popular in German-speaking academia; bought by Lumivero.
• EndNote — paid; legacy commercial standard; Word integration; site-licences common.

Hosted (paid) reference managers

• Mendeley — free + paid storage; owned by Elsevier; controversial in OA circles; UI has stagnated since the Elsevier acquisition.
• Paperpile — paid + free; Google-Docs-native; modern UI.
• ReadCube Papers — paid; PDF-reading-flavoured.
• Read by QxMD — free; medical-literature-flavoured.

Citation lookup / formatting

• CrossRef API — free; the underlying DOI metadata source.
• ZoteroBib (zbib.org) — free; one-off bibliography generator from Zotero team.
• Citation Machine / EasyBib / Cite This For Me — paid + free; consumer-grade with ads on free tier.
• Citationsy — paid + free.
• CSL Citation Style Language — open standard; 10,000+ journal styles; the lingua franca for Zotero / Mendeley / Papers.

Academic search

• ★ Semantic Scholar — free; AI-powered; AI summaries; TLDR model; the modern default. Allen Institute for AI.
• Google Scholar — free; broadest coverage; least-good metadata.
• Connected Papers — free + paid; visualise citation graphs around a paper.
• ResearchRabbit — free; "Spotify for papers"; recommendation feeds.
• Inciteful — free; citation-network exploration.
• Lens.org — free; patents + scholarly works.
• Scite.ai — paid; "smart citations" — flags whether a citation supports / contradicts.
• Elicit — paid + free; LLM-driven literature review tool.
• Consensus — paid + free; AI yes/no on research questions.
• Undermind, SciSpace — AI literature search assistants.

Paper hosting / preprints

• arXiv — free preprint server; physics, math, CS, etc.
• bioRxiv / medRxiv / chemRxiv / SocArXiv / EarthArXiv — discipline preprint servers.
• OSF (Open Science Framework) — free preprints + open-data hosting.
• Zenodo (CERN) — free; DOI-minting open archive.

Open-access / pirate (be honest)

• DOAJ (Directory of Open Access Journals) — free; legitimate OA discovery.
• CORE — free; aggregated OA full-text.
• Unpaywall — free browser extension; legally-OA versions of paywalled papers.
• Sci-Hub — legally gray; widely used by researchers in low-income countries; flag honestly: not legal in most jurisdictions but the 95th-percentile-of-academic-coverage problem is real.
• Library Genesis (LibGen) — same situation for books.

Note-taking / annotation

• Hypothes.is — free; BSD; collaborative web annotation; great for class readings.
  • https://github.com/hypothesis/h
• PDF.js + Zotero notes — Zotero 7 has best-in-class PDF annotation built in.
• Obsidian + Zotero plugin — see Notes & Wikis; the academic Obsidian workflow.
• Logseq + Zotero — same idea, outliner-flavoured.

LaTeX environments

• ★ Overleaf — free + paid; the hosted-LaTeX default; Overleaf Community Edition is AGPL self-host.
  • https://github.com/overleaf/overleaf
• TeX Live / MiKTeX — free local LaTeX distributions.
• VS Code + LaTeX Workshop — free local writing environment.
• Quarto — MIT; modern Pandoc-based academic publishing.
• Typst — Apache 2.0; modern LaTeX competitor; faster compile.
  • https://github.com/typst/typst

Pick this if…

• Default reference manager: Zotero (with WebDAV / Nextcloud sync).
• LaTeX-first workflow: JabRef.
• Already in Google Docs: Paperpile.
• Modern academic search: Semantic Scholar > Google Scholar.
• Visualise paper relationships: Connected Papers or ResearchRabbit.
• AI-driven literature review: Elicit or Consensus.
• Hosted LaTeX: Overleaf.
• Modern alternative to LaTeX: Typst.