sourcelens

sourcelens collects the latest research on any topic into one chronological catalogue. It searches PubMed, Europe PMC, arXiv and OpenAlex, downloads the open-access full texts with their figures and supplementary files, finds the code and packages the papers link to, and exports references for Zotero or LaTeX. Run it again later and it adds only what is new; notes you write in the catalogue are never overwritten.

Website: https://bhagesh-h.github.io/sourcelens/

Install

Python (3.10 or newer, any system):

pip install sourcelens

Go binary (one file, no dependencies). Linux and macOS:

curl -fsSL https://raw.githubusercontent.com/bhagesh-h/sourcelens/main/install.sh | sh

Windows (PowerShell):

irm https://raw.githubusercontent.com/bhagesh-h/sourcelens/main/install.ps1 | iex

Or download sourcelens_linux_amd64, sourcelens_linux_arm64, sourcelens_macos (Apple silicon and Intel) or sourcelens_windows_amd64.exe from the latest release. Both implementations have the same commands. To convert PDFs to text, the Go binary needs poppler (apt install poppler-utils, brew install poppler).

Use

sourcelens config set contact_email you@example.org    # once; Crossref, OpenAlex, NCBI and Unpaywall ask for it
sourcelens "CRISPR base editing"                        # start a catalogue; run again later to add what is new
sourcelens query --topic "CRISPR base editing" --range 1m
sourcelens export --topic "CRISPR base editing" --format BIB --out crispr.bib

Look first, then download only what you pick:

sourcelens "CRISPR base editing" --dry-run              # metadata and a table, no downloads
sourcelens query --topic "CRISPR base editing" --in reports/dryrun_<stamp>.csv --summary "off-target" --out picked.csv
sourcelens download --topic "CRISPR base editing" exports/picked.csv
sourcelens files --topic "CRISPR base editing" --ext xlsx,csv --copy-to ~/tables

Commas, semicolons and OR separate alternatives, every word of an alternative is required, and double quotes keep a phrase together: sourcelens '"base editing", "prime editing"'.

Each topic gets a folder such as ~/sourcelens/crispr-base-editing/, with progress.csv as the main table, and every run writes reports/runreport_<stamp>.html, a searchable page of the whole catalogue. sourcelens config set output DIR changes the folder, and sourcelens help lists every command.

Documentation

• Install options: every system, PDF extras, Docker, Python or Go
• Usage: dry run and download, files, reports, every command and option
• Outputs: the catalogue folder, attachments, the columns of progress.csv
• Configuration: settings and catalogue configuration
• Sources and limitations
• Development and publishing
• Default topic: aging clocks

License

GPL-3.0. See LICENSE.