Zotero plugin that links your Markdown database to Zotero. Jump directly from Zotero Items to connected Markdown files. Automatically tags Zotero Items so you can easily see which papers you've made notes for
“Graphviz” package produced by Sebastian Bank (available here: https://pypi.org/project/graphviz/) can be used to produce “Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA)” (Moher et al., 2009) flow chart.
Wonderful for those cases where you need the full python environment at your disposal.
Contains live graphs (using jupyter kernels), or can even include full jupyter notebooks and allow you to edit them. Contains what they call 'rabbit-hole' links which allow a reader to drill down into definitions/examples/sources.
Seems pretty neat - though I would need it to be included in Quarto (thus Pandoc) to be of real use.
Frontend for papis, allowing you to search, sort, browse through your references.
Has some advanced features for copying stuff to clipboard, sending things to vim, and is configurable with its mappings (which somewhat mimic vim to begin with).
Early development still (no support for whoosh database e.g.) but very promising!
Another bibliography manager for the command line. This one seems fairly nice: It keeps everything in plain-text (unlike papis), seems fairly customizable and extensible (unlike bibman), has some quality of life features like doi/arxiv import, git versioning and a plugin system.
Having used it a little - it is fairly nice, except for two niggling issues: with around 1000 library entries it becomes pretty sloow and it does not allow for advanced query syntax, even though it seems like it would support it. Author search only search in last names and you can not use any boolean logic to search for anything not tagged a certain way for example. These two issues are pretty major for larger libraries.
A comment on pdf annotation on unix systems. Go to the link for follow-up links to spacemacs and the layer in question:
Zathura is amazing, but if you want to take notes in a more or less zathura style pdf-editor (more than just reader), then I would recommend you to check out Spacemacs with its pdf layer. It has all features that Zathura has, but it adds very strong annotation features, it is mind blowing. You have a pdf-editor right within your vim-like editor. With org-noter you can send annotations directly to your org files (the video uses Emacs bindings, but the Spacemacs project uses a perfect Vim rebuild within Emacs). Spacemacs additionally comes with the amazing org-mode for organizing your notes. Due to the Spacemacs layer system, it is very easily installed (I assume you are on a GNU/linux type of system, as you are already using Zathura). There even exists an option to highlight using the keyboard only, although in this case I find it easier to use the mouse.
Allows you to collaborate on RMarkdown writing through google docs. You will have to use RMarkdown syntax in google docs however, which seems even more cumbersome than plaintext integrations.
As far as I can see on the demonstration, it will also not do anything for better presentation while writing (since it isn't knitting or anything before you download from gdocs again of course). Don't know how well people would adopt this then.
A really interesting open-source (and open data friendly as far as I can see) tool for writing, publishing, sharing, exporting, and interacting on (think peer review) articles and scientific writings. Can probably also be used for other writings but that's the primary intent.
Seems really interesting, as in should delve deeper with this one. Built on W3C standards uses OpenID and other interesting tidbits.
Prose diffs for any document format supported by Pandoc. Can be used to compare two different pandoc documents or, much more useful to me, to convert 'track changes' changes in an office (word, libreoffice, ..) document into criticmarkup diffs.
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The personal, minimalist, super-fast, database free, bookmarking service by the Shaarli community