Zotero
Zotero might be the solution to a problem you didn't think you had, but probably do. It is a tool for organizing, sorting, indexing, and annotating papers, books, and a lot of other media types.
This section gives a small overview of the most important features.
Media in Zotero can be organized in a folder structure.
Folders are referred to as 'collections' in Zotero and can be arbitrarily nested. The folders contain the items added, which can also be moved and duplicated per the users wishes.
All items in zotero can be accompanied by a copy of the media they are indexing. For papers this means a pdf copy of said paper, webpages can be accompanied by a snapshot of the webpage, and this holds for more media types, but these should be the most important.
Items in Zotero are supplemented by information useful for searching and referencing.
The information fields can be manually altered or corrected, and also fields can be added if necessary. The fields can also differ between media types,
meaning that a 'journal article' has different fields compared to a 'newspaper article'.
Items can contain more than just a copy of the media they represent (e.g a pdf copy of a paper). They can also contain a notes file which can be useful to quickly mark certain items.
Since version 6 of Zotero this has been greatly expanded upon. Pdf's can now be opened directly in Zotero and the viewer now also provides a multitude of marking and annotating tools to the user.
Text can now be highlighted and annotated, screenshots can be made, and postit notes can be added.
This is made even better with the new Zotero app for IOS. This gives one the ability to also annotated with the Apple pen and read directly from their device. There is also an Android app for those with an Android tablet, but this is an unofficial implementation.
Collections can be shared across different users or organizations. There is even the ability for the owner of the collection to issue different permissions, something which could be useful with courses focused on paper reading, students being granted access to a shared collection of papers, but not being able to edit this collection.
There are a few methods of synchronization. The easiest one is through the use of an account with Zotero. There are both free and paid versions, the main difference between these is the amount of storage space for synchronizing media. The free tier allows for 300MB while the higher tiers offer 2GB, 6GB, and unlimited respectively (for more information see this link). There is also the option of using a WEBDAV endpoint. This can thus be self-hosted like with Nextcloud or provided through a proxy.
The synchronization is very useful in combination with the app as it thus also syncs all the annotations made, not just the documents.
Without some of the integrations Zotero wouldn't work as well. There are two extensions which are key for having a useful workflow and I will cover both of them here. For a more detailed but probably incomplete list, see this link.
Zotero itself can create exports in the form of references of items. The most useful one is a bibtex export. This can be either exported directly to a file or be copied to the clipboard. While this is useful, it is rather limited. The 'Better bibtex' extension is an extension which has to be installed through the Zotero client. The extension provides things like better citation keys (which can be further customized if desired), and automatic export.
Especially the automatic export is useful as it can be enabled on a collection granularity. This allows one to create a collection specific for a course or project and automatically have references ready for citation in LaTeX.
The webpage for Better bibtex can be found here . For people who want true control, the extension also provides a JSON-RPC server which can be used to retrieve more information on items and collections.
This is a browser extension which is available for Chrome, Safari, and Firefox (see here). The extension allows one to save different media types directly from the browser to Zotero. This includes but is not limited to, papers, videos, and webpages. The only requirement is that you have the desktop application running when using the extension.
The extension gives you a small button which you can press in order to make a copy of the media you are looking at. This copy is then stored in the folder currently opened in the Zotero client, or to one manually selected. When available, this copy is then automatically supplemented by the relevant information. If the information cannot be found, it can be entered either using a reference like the DOI or by hand.
There are many more integrations available, like a Google Docs extension and a libreoffice plugin. Even overleaf has support for Zotero.
Searching for papers while not present at the uni building can be a bit challenging. The VU library search function is non-functional at best and often just gives you papers you are not actually looking for. Luckily Zotero can help with this as well. The Zotero connector browser extension is able to recognize proxy domains for a lot of different publishers, ACM for example is supported through this.
This link gives a bit more information, but what it comes down it is that Zotero can recognize the domain you are trying to reach and redirect you to a domain of the university which allows you to actually view the paper and download the PDF.
Configuring the proxies can be a bit annoying so I provide my configuration here:
Scheme = %h.vu-nl.idm.oclc.org/%p
Hostnames:
dl.acm.orglink.springer.comwww.acm.org
For true emacs chads there is a simple method for directly pulling references out of Zotero into org mode documents or LaTeX files. This is used through the automatic export provided by Better bibtex. Things like the orb extension allows one to directly index a bibtex file and provide links. There is configuration available to use it directly in combination with org-roam, allowing one to make node directly based on a paper, and then create a backlink.
I personally use this very often, if one interested in my configuration, let me know, then I'll provide it here.