# AI use cases for Thesys Core (Sreehari05055/thesys-core) Repo: [Sreehari05055/thesys-core](https://github.com/Sreehari05055/thesys-core) | Use cases: 4 | Page: https://dedupedai.com/use-cases/sreehari05055-thesys-core/ Thesys is an open-source local research workspace for searching open-access papers, uploading PDFs, asking cited questions, comparing papers, and exporting citations. This file holds every use case of this repo. Each one starts with a "## " heading and ends with its URL. - Ask cited questions across your own PDF library: https://dedupedai.com/use-cases/sreehari05055-thesys-core/ask-cited-questions-about-your-papers/ - Find open-access papers and add them to your library: https://dedupedai.com/use-cases/sreehari05055-thesys-core/find-and-add-open-access-papers-to-library/ - Check whether two papers agree on a specific claim: https://dedupedai.com/use-cases/sreehari05055-thesys-core/compare-two-papers-on-one-claim/ - Export your library as a bibliography file: https://dedupedai.com/use-cases/sreehari05055-thesys-core/export-bibliography-for-your-writing-tool/ ## How to ask cited questions across your own PDF library with Thesys Core Repo: [Sreehari05055/thesys-core](https://github.com/Sreehari05055/thesys-core) | Difficulty: Intermediate | Time: 90 minutes | Basis: From the README Run Thesys locally, upload papers, and get chat answers that jump to the exact passage in each PDF. **Who it is for:** A graduate student or researcher with a folder of PDFs who needs quick, sourced answers to questions about their reading list. **The problem:** Searching many PDFs by hand for one claim or method is slow, and chat answers without sources are hard to trust. **The outcome:** A running local workspace where each answer cites a passage, and clicking the citation opens the highlighted spot in the PDF. ### Steps 1. Run `cp backend/.env.example backend/.env` and set OPENAI_API_KEY and EMAIL in backend/.env. 2. Run `docker compose up --build` from the repo root and wait for the first build to finish. 3. Open http://127.0.0.1:5000 in a browser and upload one or more PDFs to the library. 4. Ask a question in chat, then click a citation to jump to the highlighted passage in the preview. 5. Run `docker compose down` when you are done. Your papers and chat history stay in the thesys-data volume. ### Prompt to paste into your agent ```text Use the Sreehari05055/thesys-core repo to set up a local research workspace with Docker, set OPENAI_API_KEY and EMAIL in backend/.env, and upload the PDFs in . Report the chat answer to the question and the citation it links to. Verify that clicking the citation opens the highlighted passage in the PDF preview. ``` ### Caveat The first ingest downloads Hugging Face weights inside the container, and chat needs an OpenAI API key, so the answers are not fully offline. Disclaimer: Third-party repos we don't own or vouch for. AI-generated use cases can be wrong: review everything and run at your own risk. Full text: https://dedupedai.com/disclaimer/ URL: https://dedupedai.com/use-cases/sreehari05055-thesys-core/ask-cited-questions-about-your-papers/ ## How to find open-access papers and add them to your library with Thesys Core Repo: [Sreehari05055/thesys-core](https://github.com/Sreehari05055/thesys-core) | Difficulty: Beginner | Time: 60 minutes | Basis: From the README Search OpenAlex and arXiv in one pool, preview records, and add the useful ones to your Thesys library. **Who it is for:** A literature reviewer starting a new topic who needs a quick list of open-access papers without checking several sites. **The problem:** Open-access papers are spread across several sources, so building a first reading list takes time. **The outcome:** A library of relevant open-access papers, each previewed and ready for chat and citation export. ### Steps 1. Run `cp backend/.env.example backend/.env` and set EMAIL in backend/.env. Add OPENALEX_API_KEY only if you have one. 2. Run `docker compose up --build` from the repo root and open http://127.0.0.1:5000. 3. Search for your topic in the Discover section to get OpenAlex and arXiv results in one list. 4. Preview a record, open its link if you want the source, and add the paper you want to your library. 5. Run `docker compose down` to stop the workspace. Added papers stay in the thesys-data volume. ### Prompt to paste into your agent ```text Use the Sreehari05055/thesys-core repo to start the Docker workspace, search Discover for , and add the five most relevant open-access papers to the library. Report the titles and links of the papers added. Verify that each added paper appears in the library list. ``` ### Caveat The README describes only open-access sources, OpenAlex and arXiv, so paywalled literature is not covered by this workflow. Disclaimer: Third-party repos we don't own or vouch for. AI-generated use cases can be wrong: review everything and run at your own risk. Full text: https://dedupedai.com/disclaimer/ URL: https://dedupedai.com/use-cases/sreehari05055-thesys-core/find-and-add-open-access-papers-to-library/ ## How to check whether two papers agree on a specific claim with Thesys Core Repo: [Sreehari05055/thesys-core](https://github.com/Sreehari05055/thesys-core) | Difficulty: Intermediate | Time: 90 minutes | Basis: From the README Select two library PDFs, turn on Compare, and see which retrieved passage pairs support or contradict a claim. **Who it is for:** A researcher writing a related-work section who needs to see where two papers agree or disagree on one result. **The problem:** Reading two long papers side by side to find where they conflict on one claim is slow and easy to get wrong. **The outcome:** A side panel listing passage pairs from both papers, each labeled corroboratory, contradictory, or neutral, with a confidence value. ### Steps 1. Run `cp backend/.env.example backend/.env` and set OPENAI_API_KEY, EMAIL, and TYPESAFE_API_KEY in backend/.env. 2. Run `docker compose up --build` from the repo root and open http://127.0.0.1:5000. 3. Upload the two papers to the library, then select both PDFs. 4. Turn Compare on, ask about one specific claim, and read the side panel of labeled pairs with confidence. 5. Open the cited passages to confirm each label before you use it in your writing. ### Prompt to paste into your agent ```text Use the Sreehari05055/thesys-core repo with a valid TYPESAFE_API_KEY to compare the two library papers and on the claim . Output the list of passage pairs with their labels and confidence values. Verify that each pair shows the matching passages in both PDFs. ``` ### Caveat Compare is unavailable without TYPESAFE_API_KEY, and the labels are model classifications that still need your reading of the passages. Risk, credentials: Compare needs a TYPESAFE_API_KEY and chat needs an OPENAI_API_KEY in backend/.env, so keep that file out of shared repos and screenshots. Disclaimer: Third-party repos we don't own or vouch for. AI-generated use cases can be wrong: review everything and run at your own risk. Full text: https://dedupedai.com/disclaimer/ URL: https://dedupedai.com/use-cases/sreehari05055-thesys-core/compare-two-papers-on-one-claim/ ## How to export your library as a bibliography file with Thesys Core Repo: [Sreehari05055/thesys-core](https://github.com/Sreehari05055/thesys-core) | Difficulty: Beginner | Time: 45 minutes | Basis: From the README Turn your Thesys library into BibTeX, RIS, EndNote, or CSV for your writing or reference manager. **Who it is for:** A writer preparing a thesis or paper who needs the reference list in the format their editor or manager expects. **The problem:** Retyping citations for each source wastes time and introduces errors in the bibliography. **The outcome:** A bibliography file in the format you choose, ready to import into your writing tool. ### Steps 1. Run `docker compose up --build` from the repo root and open http://127.0.0.1:5000. 2. Open the library and select the papers you want to cite. 3. Choose the export option and pick BibTeX, RIS, EndNote, or CSV. 4. Import the downloaded file into your reference manager or LaTeX project and check a few entries against the source. 5. Run `docker compose down` to stop the workspace when you finish. ### Prompt to paste into your agent ```text Use the Sreehari05055/thesys-core repo to open the library, select the papers on the topic , and export them as . Output the file name and entry count. Verify that the file opens and contains one entry per selected paper. ``` ### Caveat The README does not say how entries are filled in for every paper, so check the metadata in each exported entry before submitting work. Disclaimer: Third-party repos we don't own or vouch for. AI-generated use cases can be wrong: review everything and run at your own risk. Full text: https://dedupedai.com/disclaimer/ URL: https://dedupedai.com/use-cases/sreehari05055-thesys-core/export-bibliography-for-your-writing-tool/