// Software stack
Paper reading & research
Read papers, survey literature, run experiments and take notes.
4 pieces4 setup stepsscenario: Research: find, read and review literature
What goes in it
- 1
NotebookLM AI notes & knowledge management Closed / commercial
Reading
Google's source-grounded notebook for Q&A, summaries and audio overviews.
Or: PDFMathTranslate · llm-for-zotero · BabelDOC
- 2 ★ 20k
DeepResearch AI search & research Open source
Research agent
Tongyi Deep Research, an open-source deep research agent.
Or: feynman · OpenResearch · deep-research
- 3 ★ 54k
scientific-agent-skills Skills & rules Open source
Skills
Science skill library that turns agents into research assistants.
- 4
Obsidian AI notes & knowledge management Closed / commercial
Notes
Local Markdown notes and personal knowledge base; plugins connect AI and agents.
Or: siyuan · open-knowledge
How to set it up
- 01Collect PDFs in Zotero or a folder
- 02Add paper translation and summarisation
- 03Use a research agent for multi-source surveys
- 04Write results back into your knowledge base