literature management for bio programmers

Related tags

Miscellaneous seneca
Overview

Seneca 🏛️

https://en.wikipedia.org/wiki/Seneca_the_Younger

This uses sci-hub, which is probably illegal.

Literature indexing, search, and note management for bio programmers.

Quickstart

To install:

git clone https://github.com/kennyworkman/seneca
brew install zathura
make build

To add a paper:

seneca https://www.nature.com/articles/s41467-020-18008-4

To manually add a paper (if scraping fails):

seneca raw

To search across indexed papers and retrieve note buffer:

seneca l 
# or
seneca letters

I think you will find this is all that you need. There is no delete. If you spent enough time indexing a reference, I'm of the opinion you should hang on to it (just in case).

Notes persist across time. Opening a long forgotten paper weeks later will recover time stamped notes from my last interaction with it.

Design

Special attention towards:

  • decentralized structure
  • low mental transaction cost on note read/write
  • speed
  • terminal based workflow with hackable internals

Assumes text editor of choice is vim. Good synergy with tiling window managers.

Read more here.

Debt

  • Non-filesystem persistence - sqlite3
  • Support for non DOI-based references:
    • market research
    • books
    • technical preprints
  • Integration with other tools:
    • Automatic indexing of relevant papers at spaced interval
    • Priority list / backlog of desired reading
    • Automatic presentation of backlog depending on calendar events
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