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Zotero integrates with my academic workflow linking notes with citations and providing links, backlinks, tags, and collections. I previously used EndNote for academic note-taking but it is expensive and not open-source. Although other note-taking software may provide some features like free-form hierarchical organization (Zotero is alphanumeric) and easy export to .txt or .md (Zotero exports to html), the integration of powerful note-taking capabilities in this open-source bibliographic database app makes it preferable to standalone note-taking apps like Simplenote, Cherrytree, Zkn3, or nvAlt. Zotero also performs very well on all main platforms. See More
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When it comes to managing tasks, I'll keep preaching it. See More
Evernote is designed to make it easy to keep your notes well organized, which aids in quickly finding/browsing old information. You can put notes into a single notebook and use search to access old notes, or if you're so inclined, organize notes extensively with hierarchical notebooks and tags. See More