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README: real-world multi-session context + shareable repro packages
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README.md

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### Long-Term Memory
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Cross-session memory via [MemPalace](https://github.com/AidanCooper/mempalace) (ChromaDB-backed). Every analysis decision, parameter choice, and conversation is stored with metadata (branch, timestamp, analysis phase). When the agent needs to recall a past decision — "why did we choose resolution 0.8?" — it does a semantic search and retrieves the relevant context, even across sessions.
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Real-world scRNA-seq analysis happens over weeks — you run QC on Monday, come back to clustering on Thursday, and a reviewer asks about your normalization choice a month later. scAgent maintains cross-session memory via [MemPalace](https://github.com/AidanCooper/mempalace) (ChromaDB-backed) so nothing is lost between sessions. Every analysis decision, parameter choice, and conversation is stored with metadata (branch, timestamp, analysis phase). When the agent needs to recall a past decision — "why did we choose resolution 0.8?" — it does a semantic search and retrieves the relevant context, even from weeks ago.
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### Provenance & Reproducibility
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Every tool invocation is recorded as a W3C PROV-O graph in JSON-LD — inputs, parameters, outputs, software versions, timestamps. Full traceability.
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The export module ([`scagent/export.py`](scagent/export.py)) generates from the provenance chain:
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- **Methods section** — camera-ready prose for a paper, auto-generated from provenance records
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- **Reproducibility package**`methods.md`, `params.json`, `README.md`, and `replay.py` (a script that re-runs the entire analysis from raw data using the recorded parameters)
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- **Reproducibility package** — a self-contained directory with `methods.md`, `params.json`, `README.md`, and `replay.py` (a script that re-runs the entire analysis from raw data using the recorded parameters)
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Share the reproducibility package with a collaborator or reviewer and they can reproduce your exact analysis independently — same parameters, same tool versions, same results.
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### Biologist-Friendly
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