Update: I now use Zotero as reference manager which fulfills many of the needs listed below. I leave the code here because it was a fun project.
I use Mendeley to manage my citations. One limitation of this (and to my knowledge any other) reference manager is that you cannot link between papers. For that reason I wrote summaries in LaTeX in which I included hyperlinks to articles (e.g., if they would complement or contradict each other). This approach worked well in the beginning but did not scale well. At not even 100 summaries compiling took over a minute.
Another solution was required… and here comes TiddlyWiki!
TiddlyWiki is a “unique non-linear notebook for capturing, organising and sharing complex information.” It’s general plus points are, among others:
Non-linearity: link from any entry to any other entry. Clicking a link opens the entry in a card. Read the card, close it, and continue reading where you left off.
Scale and speed: No problems with hundreds of summaries.
Ease of use. The wiki is a single
.htmlfile that you edit in your browser. No installation required. Markdown makes editing child’s play.
And many more…