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Biomedical research agent with 28 MCP tools powered by MedGemma, TxGemma and OpenCode

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The open source biomedical research agent.

[![MedSci Agent running a single-cell RNA-seq pipeline in OpenCode](https://raw.githubusercontent.com/omar-A-hassan/medsci-agent/main/docs/demo.png)](https://www.kaggle.com/competitions/med-gemma-impact-challenge)

MedSci Agent gives any LLM access to 28 biomedical and execution tools — drug ADMET prediction, protein structure search, single-cell RNA-seq analysis, medical image interpretation, literature search, policy-controlled document acquisition, and isolated sandbox execution — all powered by [MedGemma](https://huggingface.co/google/medgemma-4b-it), [TxGemma](https://huggingface.co/google/txgemma-2b-predict) running locally via Ollama, and [OpenCode](https://opencode.ai). No data leaves your machine.

Built for the [MedGemma Impact Challenge](https://www.kaggle.com/competitions/med-gemma-impact-challenge).

---

## Quick Start

Once [setup](#setup) is complete and Ollama is running, open the project in [OpenCode](https://opencode.ai) and try:

**Drug discovery:**
> Analyze the drug-likeness of ibuprofen (CC(C)Cc1ccc(cc1)C(C)C(=O)O) and predict its ADMET properties.

![Drug discovery and ADMET prediction demo](https://raw.githubusercontent.com/omar-A-hassan/medsci-agent/main/docs/drug_demo.gif)

**Single-cell omics:**
> Read my H5AD file, preprocess it, cluster with Leiden at resolution 0.5, and run differential expression.

![Single-cell omics demo](https://raw.githubusercontent.com/omar-A-hassan/medsci-agent/main/docs/omics_demo.gif)

**Literature search:**
> Search PubMed for recent papers on CRISPR-Cas9 gene therapy for sickle cell disease.

![Literature demo](https://raw.githubusercontent.com/omar-A-hassan/medsci-agent/main/docs/Literature_demo.gif)

The Agent automatically selects the right tools, calls MedGemma for interpretation, and returns a synthesized answer.

---

## Architecture

You bring your own LLM. Configure any model in OpenCode (via `/model`) and it becomes the orchestrator — it reads your query, selects the right tools, calls them through MCP, and synthesizes the results. The MCP servers handle the domain logic underneath.

```
Cloud LLM (user's choice via OpenCode)
    |
    | tool calls via MCP
    v
+--- MCP Servers (Bun / TypeScript) ---+
|                                       |
|  server-drug        5 tools           |
|  server-protein     5 tools           |
|  server-literature  4 tools           |
|  server-acquisition 2 tools           |
|  server-imaging     1 tool            |
|  server-omics       5 tools           |
|  server-paperqa     1 tool            |
|  server-sandbox     5 tools           |
|                                       |
+-------+-------------------+-----------+
        |                   |
        v                   v
   Ollama (local)     Python Sidecar
   - MedGemma 4B      - RDKit
   - TxGemma 2B       - BioPython
                       - Scanpy
```

**MedGemma** interprets tool outputs — it reads raw data from APIs and computational tools, then provides clinically relevant summaries. Every tool that calls MedGemma returns a `model_used` flag and degrades gracefully if the model is unavailable.

**TxGemma** predicts ADMET properties (absorption, distribution, metabolism, excretion, toxicity). It runs exact prompt templates from the [Therapeutics Data Commons](https://tdcommons.ai) and outputs binary classifications for six safety endpoints.

The **Python sidecar** is a long-running process that pre-imports scientific libraries and handles requests over stdin/stdout via JSON-RPC. This avoids the 2–5 second startup cost of importing RDKit or Scanpy on every call.

**`synthesize` parameter:** Every drug, protein, and omics tool accepts an optional `"synthesize": false` input field. When `false`, the tool skips the MedGemma interpretation step and returns raw data immediately. This is useful when you want fast data-only results, or when Ollama is unavailable. Default is `true` (synthesis enabled).

---

## Tools

### Drug Discovery (server-drug)

| Tool | Description | Backend |
|------|-------------|---------|
| `analyze_molecule` | Physicochemical properties from SMILES (MW, LogP, TPSA, HBD/HBA, rings, formula) | RDKit + MedGemma |
| `lipinski_filter` | Lipinski Rule of Five drug-likeness check | RDKit |
| `molecular_similarity` | Tanimoto similarity between two molecules using Morgan fingerprints | RDKit |
| `predict_admet` | BBB penetration, intestinal absorption, hERG blocking, CYP3A4 inhibition, Ames mutagenicity, DILI risk | TxGemma + RDKit + MedGemma |
| `search_chembl` | Search ChEMBL for bioactive molecules and targets | ChEMBL API + MedGemma |

### Protein Analysis (server-protein)

| Tool | Description | Backend |
|------|-------------|---------|
| `parse_fasta` | Parse FASTA files, return sequence metadata | BioPython |
| `analyze_sequence` | Sequence length, composition, molecular weight | BioPython + MedGemma |
| `search_uniprot` | Search UniProt by gene, protein name, or accession | UniProt API + MedGemma |
| `search_pdb` | Search PDB for 3D structures by protein or PDB ID | RCSB PDB API + MedGemma |
| `predict_structure` | Retrieve AlphaFold predicted structure and confidence scores | AlphaFold DB API + MedGemma |

### Literature, Acquisition & Synthesis (server-literature, server-acquisition & server-paperqa)

| Tool | Description | Backend |
|------|-------------|---------|
| `search_pubmed` | Search PubMed with Boolean and MeSH queries | NCBI E-utilities + MedGemma |
| `fetch_abstract` | Fetch full abstract and metadata by PMID | NCBI E-utilities + MedGemma |
| `search_openalex` | Search OpenAlex for scholarly works, citations, open access status | OpenAlex API + MedGemma |
| `search_clinical_trials` | Search ClinicalTrials.gov by condition, drug, or intervention | ClinicalTrials.gov API + MedGemma |
| `resolve_identifier_to_sources` | Resolve DOI/PMID/PMCID into candidate source URLs with provenance and confidence | NCBI ID Converter + deterministic transforms |
| `acquire_documents` | Policy-controlled document retrieval from DOI/PMID/PMCID/URL with content-level labeling and explicit extraction backend metadata (`pmid/pmcid`: BioC-first with Scrapling fallback, `doi/url`: Scrapling-primary) | NCBI BioC + Scrapling sidecar + safety policy engine |
| `search_and_analyze` | Deep semantic synthesis of up to 10 identifiers/documents (internal NCBI acquisition or pre-acquired documents) using contextual LLM re-ranking | PaperQA2 + Tantivy |

### Medical Imaging (server-imaging)

| Tool | Description | Backend |
|------|-------------|---------|
| `analyze_medical_image` | Analyze X-ray, CT, pathology, or dermatology images (PNG/JPEG, max 50 MB) | MedGemma (multimodal) |

### Omics (server-omics)

| Tool | Description | Backend |
|------|-------------|---------|
| `read_h5ad` | Load H5AD file, return observation and variable metadata | Scanpy |
| `preprocess_omics` | Filter, normalize, log-transform, find highly variable genes | Scanpy |
| `cluster_cells` | Leiden or Louvain clustering with UMAP coordinates | Scanpy |
| `differential_expression` | Differential expression between groups (Wilcoxon, t-test, logreg) | Scanpy + MedGemma |
| `gene_set_enrichment` | Pathway enrichment against MSigDB, GO, KEGG via Enrichr | Enrichr API + MedGemma |

### Sandbox Execution (server-sandbox)

| Tool | Description | Backend |
|------|-------------|---------|
| `sandbox_prepare` | Create/reuse a Docker sandbox with default `network_policy=deny` | Docker Sandbox CLI |
| `sandbox_run_job` | Execute command in sandbox with deterministic timeout + logs | Docker Sandbox CLI |
| `sandbox_status` | Check sandbox state (`running`/`stopped`/`unknown`) with retry/backoff | Docker Sandbox CLI |
| `sandbox_fetch_artifact` | Read artifact/log content with size/path safety constraints | Host file access + safety checks |
| `sandbox_teardown` | Stop or remove sandbox | Docker Sandbox CLI |

---

## Setup

### Fresh install — complete sequence

```bash
# 1. Install Bun and uv (if not already installed)
curl -fsSL https://bun.sh/install | bash
curl -LsSf https://astral.sh/uv/install.sh | sh

# 2. Clone and install JS/TS dependencies
git clone https://github.com/omar-A-hassan/medsci-agent.git
cd medsci-agent
bun install

# 3. Create Python environments
bun run setup:py:core     # RDKit + BioPython + Scanpy → .venv/
bun run setup:py:paperqa  # PaperQA + Scrapling + ACE → packages/server-paperqa/.venv-paperqa/

# 4. Pull Ollama models (Ollama must be installed first: https://ollama.com)
ollama pull medgemma:latest
ollama pull mxbai-embed-large
ollama pull hf.co/matrixportalx/txgemma-2b-predict-GGUF:Q4_K_M

# 5. (Optional) Export API keys for cloud features — do this BEFORE starting OpenCode
export OPENROUTER_API_KEY="sk-or-..."   # needed for ACE MCP and cloud PaperQA
export ANTHROPIC_API_KEY="sk-ant-..."  # only if using Anthropic directly

# 6. Verify setup
bun run typecheck
bun test

# 7. Open in OpenCode
opencode  # MCP servers start automatically via opencode.json
```

The `opencode.json` is pre-configured for local-only use (Ollama + local Python). No additional configuration is needed for the core tools. See the sections below for cloud model setup and optional features.

---

### Prerequisites

- [Bun](https://bun.sh) >= 1.1
- [uv](https://docs.astral.sh/uv/) (Python package and environment manager)
- [Ollama](https://ollama.com)
- [OpenCode](https://opencode.ai)
- **Docker Desktop 4.40+** with the **Docker AI Sandbox** feature enabled (required for sandbox tools only)
  - The `sandbox_*` tools use `docker sandbox` subcommands — a first-party feature in Docker Desktop 4.40+. Enable it under _Settings → Features in Development → Docker AI Sandbox_.
  - All other tools work without Docker.

> **Sandbox not available?** If you don't have Docker Desktop 4.40+ you can still use all 23 non-sandbox tools. Leave the `medsci-sandbox` MCP server enabled — calls to sandbox tools will return clear errors rather than crashing.

### 1. Clone and install

```bash
git clone https://github.com/omar-A-hassan/medsci-agent.git
cd medsci-agent
bun install
```

### 2. Python environments

The system uses two strictly decoupled Python virtual environments, both managed with `uv`.

**Core Environment (Required):**
```bash
bun run setup:py:core
```

**PaperQA + Acquisition Environment (Required for strict full-text retrieval and deep synthesis):**
```bash
bun run setup:py:paperqa
```

Or run both in one command:

```bash
bun run setup:py:all
```

> **Important:** Set `MEDSCI_PYTHON` to `.venv/bin/python3` for core tools. Both `medsci-paperqa` and `medsci-acquisition` should run with `packages/server-paperqa/.venv-paperqa/bin/python3` to keep Scrapling and PaperQA dependencies in one environment.
>
> Dependency ownership:
> - `.venv` (uv groups: `scientific`, `test`): core science sidecars (RDKit/BioPython/Scanpy and related tool stacks).
> - `packages/server-paperqa/.venv-paperqa` (uv groups: `paperqa`, `ace`, `test`): PaperQA + acquisition parsing + ACE stack.

### 3. Pull Ollama models

```bash
ollama pull medgemma:latest                                      # Biomedical interpretation
ollama pull mxbai-embed-large                                    # Document embeddings for PaperQA
ollama pull hf.co/matrixportalx/txgemma-2b-predict-GGUF:Q4_K_M  # ADMET prediction
```

If `medgemma:latest` is not available directly, pull the GGUF from HuggingFace and alias it:

```bash
ollama pull hf.co/unsloth/medgemma-4b-it-GGUF:Q4_K_M
cp ~/.ollama/models/manifests/hf.co/unsloth/medgemma-4b-it-GGUF/Q4_K_M \
   ~/.ollama/models/manifests/registry.ollama.ai/library/medgemma/latest
```

> **Note:** The `cp` command creates an alias so the code can reference the model as `medgemma:latest` regardless of how it was downloaded.

### 4. Configure OpenCode

The included `opencode.json` is pre-configured. Set the `model` field to your preferred cloud LLM:

```json
{
  "model": "openai/gpt-4o"
}
```

Update the `MEDSCI_PYTHON` path in each server's environment block if your virtual environment is in a different location.

### 4.1 Optional: Enable ACE MCP (self-improvement layer)

MedSci now supports optional ACE MCP integration for adaptive strategy learning.

Install ACE MCP in the PaperQA/acquisition virtual environment (recommended):

```bash
bun run setup:py:paperqa
```

Configured MCP server name: `ace-mcp` (in `opencode.json`)

ACE model default: `openrouter/arcee-ai/trinity-large-preview:free` (set via `ACE_MCP_DEFAULT_MODEL` in `opencode.json`). This is a free OpenRouter model that requires `OPENROUTER_API_KEY`. To change:

```bash
export ACE_MCP_DEFAULT_MODEL="your/provider-model"
```

Credential model for ACE:
- ACE runs as a separate MCP process and needs provider credentials available in that process environment.
- If you use OpenAI for ACE, export `OPENAI_API_KEY` before starting OpenCode.
- If you use Anthropic/Gemini/Mistral/etc for ACE, set the corresponding provider key env var.
- ACE can use the same cloud provider/model family you use in OpenCode, but it does not automatically inherit the currently selected chat model unless you configure `ACE_MCP_DEFAULT_MODEL` accordingly.
- ACE in this setup is intentionally decoupled from local MedSci models (`medgemma`, `txgemma`, PaperQA embedding model) and should not use them unless you explicitly reconfigure it.

Default behavior in MedSci:
- in-run reflection is read-only (`ace.ask` / `ace.skillbook.get`)
- automatic post-run learning is triggered by plugin guardrails (gated by evidence quality)
- manual fallback remains available via `/ace-learn`

Skillbooks are persisted under `.opencode/ace/skillbooks/`.

Why ACE is installed in `packages/server-paperqa/.venv-paperqa` (not the core `.venv`):
- ACE learning is orchestration/synthesis logic, closest to the PaperQA + acquisition stack.
- Keeping ACE out of the core scientific sidecar avoids dependency drift for RDKit/Scanpy/BioPython workflows.
- This preserves strict environment separation and reduces breakage risk in domain toolchains.

Example override:

```bash
export ACE_MCP_DEFAULT_MODEL="anthropic/claude-3-5-sonnet-latest"
export ANTHROPIC_API_KEY="..."
```

> **Key export timing:** API keys must be exported in the shell _before_ starting OpenCode. MCP server processes are spawned at startup and inherit env from that moment — changing env vars afterwards has no effect until OpenCode is restarted.

### 5. Run tests

```bash
bun run test:all
```

This runs:
- all Bun tests across MCP servers (including sidecar-in-loop tests when `packages/server-paperqa/.venv-paperqa` exists),
- and PaperQA Python tests using the PaperQA venv interpreter.

### 6. Start

Make sure Ollama is running, then open the project directory in OpenCode. The MCP servers start automatically.

---

## OpenCode Agent Usage

### Agent roles

- `medsci` is the primary orchestrator for cross-domain workflows.
- `drug`, `protein`, `omics`, and `imaging` are focused subagents for domain-deep tasks.
- All agents follow a planning-first contract (brief plan before first tool call, then strict sequential execution).

### Built-in project commands

This repo ships OpenCode slash commands under `.opencode/commands`:

- `/triage` — classify request and propose minimal sequential MCP plan
- `/lit-deep` — literature discovery + PaperQA deep synthesis workflow
- `/sandbox-job` — sandbox lifecycle run (`prepare → run_job → status(advisory) → fetch → teardown`)
- `/qc-check` — maker-checker quality gate on scientific outputs
- `/handoff-report` — compact handoff for next agent/human
- `/ace-learn` — manual ACE learning fallback/override for a completed task
- `/ace-strategies` — inspect ACE strategy state for a domain/session

### Sandbox command default

For inline script execution, prefer:

```bash
python3 -c "print('sandbox smoke ok')"
```

instead of `python -c ...` to avoid environment-path variability across sandbox templates.

### Determinism and status policy

- Treat `sandbox_run_job` success/failure as source-of-truth for execution outcome.
- Treat `sandbox_status` as advisory state signal.
- Backend applies status retry/backoff before returning `unknown`.

---

## Configuration

Environment variables (set in `opencode.json` under each server's `environment`):

| Variable | Default | Description |
|----------|---------|-------------|
| `MEDSCI_PROFILE` | `standard` | Hardware profile: `lite`, `standard`, or `full` |
| `MEDSCI_PYTHON` | `python3` | Path to Python binary (use `.venv/bin/python3` for the virtual environment) |
| `MEDSCI_OLLAMA_URL` | `http://127.0.0.1:11434` | Ollama API endpoint |
| `MEDSCI_OLLAMA_MODEL` | `medgemma:latest` | Default Ollama model for interpretation |
| `MEDSCI_OLLAMA_TIMEOUT` | `120000` | Ollama request timeout in milliseconds |
| `MEDSCI_PYTHON_TIMEOUT` | `60000` | Python sidecar request timeout in milliseconds |
| `PQA_LLM_MODEL` | `ollama/medgemma:latest` | LLM model PaperQA uses for summarization/answering (litellm format) |
| `PQA_EMBEDDING_MODEL` | `ollama/mxbai-embed-large` | Embedding model PaperQA uses for document indexing |
| `PQA_OLLAMA_URL` | `http://localhost:11434` | Ollama endpoint for PaperQA (separate from core) |
| `PQA_EMAIL` | `medsci-agent@localhost` | Email for NCBI API access (required by NCBI usage policy) |
| `PQA_USE_DOC_DETAILS` | `false` | If `true`, enables PaperQA metadata inference during indexing (less reliable with local models) |
| `PQA_CHUNK_CHARS` | `1200` | Default chunk size (characters) for PaperQA document reader before embedding |
| `PQA_CHUNK_OVERLAP` | `100` | Overlap (characters) between adjacent chunks |
| `PQA_CHUNK_MIN_CHARS` | `400` | Lower bound for automatic chunk-size backoff retries on embedding context errors |
| `PQA_CHUNK_BACKOFF_RETRIES` | `3` | Number of times to retry indexing with smaller chunks on embed context-limit errors |
| `PQA_ACQUIRE_CONCURRENCY` | `3` | Max concurrent NCBI acquisition requests in PaperQA |
| `PQA_MAX_TEXT_CHARS` | `1500000` | Hard cap on acquired paper text size (chars) to avoid indexing blowups |
| `PQA_NEGATIVE_CACHE_TTL_HOURS` | `24` | TTL for acquisition negative-cache entries (failed sources) |
| `PQA_LLM_TIMEOUT_SECONDS` | `180` | Timeout (seconds) for LLM and summary LLM requests via LiteLLM. Sidecar timeout auto-adjusts above this. |
| `PQA_ANSWER_MAX_SOURCES` | `5` | Maximum number of sources PaperQA includes in a synthesized answer |
| `PQA_EVIDENCE_K` | `10` | Number of evidence chunks PaperQA gathers before answering |
| `PQA_DOCSET_CACHE_MAX_ENTRIES` | `8` | Max number of in-memory docset cache entries per workspace |
| `PQA_DOCSET_CACHE_MAX_BYTES` | `209715200` | Max total bytes for in-memory docset cache (default 200 MB) |
| `PQA_PREFLIGHT_CACHE_TTL_SECONDS` | `300` | TTL for cached Ollama preflight checks to avoid repeated startup latency |
| `PQA_SKIP_PREFLIGHT` | `false` | If `true`, skip Ollama model reachability/model-presence preflight checks |
| `PQA_ENABLE_DOCUMENT_INPUT` | `true` | If `false`, rejects `documents` payloads and only allows identifier-based acquisition |
| `PQA_LLM_BACKEND` | `ollama` | LLM backend for PaperQA: `ollama` (local), `openrouter`, or `anthropic` (cloud). Cloud backends skip Ollama preflight entirely. |
| `PQA_CLOUD_MODEL` | _(backend default)_ | Cloud model name in LiteLLM format when `PQA_LLM_BACKEND` is `openrouter` or `anthropic` (e.g. `openrouter/anthropic/claude-3-5-sonnet`, `anthropic/claude-opus-4-5`) |
| `PQA_QUERY_TIMEOUT_MS` | _(auto-calculated)_ | Direct override for PaperQA total query timeout in milliseconds (caps at 540,000 ms). Overrides the automatic per-paper calculation. |

Acquisition-related environment variables (optional, `server-acquisition`):

| Variable | Default | Description |
|----------|---------|-------------|
| `ACQ_REQUIRE_SCRAPLING` | `false` | If `true`, acquisition sidecar health check and HTML extraction hard-fail when Scrapling is unavailable. Default `false` enables graceful fallback to BeautifulSoup/regex. |
| `ACQ_PYTHON` | _unset_ | Optional explicit Python binary for acquisition sidecar (defaults to PaperQA venv path) |
| `ACQ_CACHE_DIR` | `.opencode/acquired_docs` | Cache location for acquired document payloads |
| `ACQ_MAX_BYTES_HARD_CAP` | `10000000` | Hard upper bound on response body bytes regardless of per-call options |

Sandbox-related environment variables (optional, `server-sandbox`):

| Variable | Default | Description |
|----------|---------|-------------|
| `MEDSCI_SANDBOX_DEFAULT_TEMPLATE` | _unset_ | Optional default Docker sandbox template |
| `MEDSCI_SANDBOX_PULL_TEMPLATE` | `missing` | Template pull policy: `missing`, `always`, `never` |
| `MEDSCI_SANDBOX_ARTIFACT_ROOT` | `sandbox-artifacts` | Artifact root directory for run logs/metadata |
| `MEDSCI_SANDBOX_DEFAULT_TIMEOUT_SEC` | `600` | Default run timeout (seconds) |
| `MEDSCI_SANDBOX_MAX_TIMEOUT_SEC` | `3600` | Max allowed run timeout (seconds) |
| `MEDSCI_SANDBOX_STATUS_RETRY_ATTEMPTS` | `2` | Number of status retries before returning `unknown` |
| `MEDSCI_SANDBOX_STATUS_RETRY_BACKOFF_MS` | `1000` | Milliseconds between status retries |

### OpenCode policy hardening (included)

`opencode.json` includes baseline hardening:

- `edit`, `task`, `skill`, `webfetch`, `external_directory`, `doom_loop` default to `ask`
- `bash` allowlist for safe read-only/dev commands
- `bash` denylist for destructive actions (`rm *`, `git push*`)
- agent-specific task/skill permission scoping for `medsci`

### Plugin guardrails (included)

Project plugin: `.opencode/plugins/medsci-guardrails.ts`

- Blocks reading sensitive `.env` files via the `read` tool (allows `.env.example`)
- Logs tool telemetry (`tool`, `session_id`, `duration_ms`, `failed`) via `client.app.log`
- Adds ACE telemetry tags (`ace_tool`, `ace_learning_write`) for auditability
- Triggers automatic post-run `/ace-learn` command execution when high-signal tool evidence is present

The `MEDSCI_PROFILE` setting controls which Python libraries are pre-imported when the sidecar starts. All tools work regardless of profile — the sidecar imports libraries lazily on first use — but pre-importing avoids a cold-start delay on the first call.

| Profile | Pre-imported | Use case |
|---------|--------------|----------|
| `lite` | RDKit | Drug discovery tools only, lower memory usage |
| `standard` | RDKit, Scanpy, BioPython, leidenalg, igraph, pynndescent | Most workflows |
| `full` | All available | Fastest first-call latency across all tools |

### PaperQA Data Nuances
When querying papers via `server-paperqa`, the tool performs a multi-step pipeline:
1. **Text Acquisition** — Full-text articles are acquired via the NCBI BioC PMC API (DOIs, PMIDs, or PMCIDs). Papers not in PMC Open Access fall back to abstract-only via the BioC PubMed API. Acquired text is cached as `.txt` files in `.opencode/pqa_papers/`.
   - `search_and_analyze` also accepts pre-acquired `documents` payloads. When provided, PaperQA skips internal acquisition and indexes those documents directly.
2. **Indexing** — PaperQA2 indexes the text files and builds a search index in `.opencode/pqa_index/`.
3. **RAG Synthesis** — The query runs against indexed chunks using Ollama for both summarization and final answer generation.

- **Models (local)**: PaperQA uses `PQA_LLM_MODEL` (default: `ollama/medgemma:latest`) for summarization and answering, and `PQA_EMBEDDING_MODEL` (default: `ollama/mxbai-embed-large`) for document embeddings. Both run locally via Ollama.
- **Models (cloud)**: Set `PQA_LLM_BACKEND=openrouter` or `PQA_LLM_BACKEND=anthropic` to route the LLM calls to a cloud provider instead of Ollama. The embedding model always stays local. Export the corresponding API key before starting OpenCode:
  ```bash
  # OpenRouter (supports many models)
  export PQA_LLM_BACKEND=openrouter
  export PQA_CLOUD_MODEL="openrouter/anthropic/claude-3-5-sonnet"
  export OPENROUTER_API_KEY="sk-or-..."

# Anthropic direct
  export PQA_LLM_BACKEND=anthropic
  export PQA_CLOUD_MODEL="anthropic/claude-opus-4-5"
  export ANTHROPIC_API_KEY="sk-ant-..."
  ```
  Cloud backends skip the Ollama LLM preflight check and tend to be significantly faster for synthesis. The acquisition and embedding steps still run locally.
- **Preflight**: The sidecar verifies Ollama reachability and required model presence before indexing/query. Failures return structured codes (`OLLAMA_UNREACHABLE`, `MODEL_NOT_FOUND`).
- **Agent Type**: Uses `"fake"` agent mode (deterministic search → gather evidence → answer path) rather than an LLM-driven agent, which reduces token usage.
- **Paper Limits**: The `search_and_analyze` schema strictly bounds processing to 10 inputs per call (papers or documents) to avoid Out-of-Memory crashes.
- **Document Provenance Contract**: Pre-acquired documents can include `extraction_backend` (`scrapling`, `beautifulsoup`, `regex`, `pdf_text`, `plain_text`) and `fallback_used` so downstream synthesis can reason about evidence quality explicitly.
- **PMC Open Access Coverage**: Full-text retrieval requires papers to be in the PMC Open Access subset (~3.5M articles). Papers outside this subset get abstract-only indexing — the response includes an `acquisition_summary` showing which papers were full-text vs abstract-only.
- **Stage-Gated Responses**: `search_and_analyze` now returns `stage_status` (`acquire`, `index`, `query`) and fail-soft terminal codes (`ACQUIRE_NONE_SUCCESS`, `INDEX_ZERO_SUCCESS`, `API_AUTH_FAILED`) instead of opaque failures. `API_AUTH_FAILED` means the cloud LLM API key was missing or rejected — check `OPENROUTER_API_KEY` / `ANTHROPIC_API_KEY`.
- **Embedding Context Guardrail**: Indexing now uses conservative chunk defaults and automatic chunk-size backoff retries when Ollama embedding rejects large inputs (`/api/embed` context-limit errors).
- **Caching**: Paper acquisition uses canonicalized identifier hashing + manifests. Index/query path includes in-memory docset cache and persisted manifests under `.opencode/pqa_index/manifest.json`.
- **Stateful Indexes**: Do **not** manually delete `.opencode/pqa_index/` or `.opencode/pqa_papers/` while a PaperQA query is in progress.

---

## Troubleshooting

### `OLLAMA_UNREACHABLE` — PaperQA or MedGemma fails to connect
Ollama must be running before OpenCode starts. MCP server processes inherit the environment at startup — run `ollama serve` first, then open OpenCode. Verify with:
```bash
curl http://localhost:11434/api/tags
```

### `MODEL_NOT_FOUND` — Model missing
Pull the required model:
```bash
ollama pull medgemma:latest
ollama pull mxbai-embed-large
ollama pull hf.co/matrixportalx/txgemma-2b-predict-GGUF:Q4_K_M
```
If `medgemma:latest` resolves but the sidecar still says `MODEL_NOT_FOUND`, the `PQA_LLM_MODEL` env var may reference a different name than what Ollama has. Check with `ollama list`.

### `API_AUTH_FAILED` — Cloud PaperQA authentication error
The API key for `PQA_LLM_BACKEND` was not found or is invalid. Export it in the shell **before** starting OpenCode:
```bash
export OPENROUTER_API_KEY="sk-or-..."   # for PQA_LLM_BACKEND=openrouter
export ANTHROPIC_API_KEY="sk-ant-..."  # for PQA_LLM_BACKEND=anthropic
```

### `ACQUIRE_NONE_SUCCESS` — PaperQA couldn't fetch any papers
The papers may not be in PMC Open Access. PaperQA falls back to abstract-only indexing for papers outside PMC OA (~3.5M articles). If you have access to the full text, use `acquire_documents` first to get pre-acquired `documents`, then pass them directly to `search_and_analyze`.

### Python sidecar tools fail (drug/protein/omics)
The core Python environment may not be set up:
```bash
bun run setup:py:core    # installs RDKit, BioPython, Scanpy into .venv/
```
Then verify `MEDSCI_PYTHON` in `opencode.json` points to `.venv/bin/python3`.

### Scrapling warning in acquisition
If you see `SCRAPLING_REQUIRED` in logs, the acquisition sidecar is running without Scrapling. This is normal — `ACQ_REQUIRE_SCRAPLING=false` (the default) lets it fall back to BeautifulSoup/regex HTML extraction. To enable Scrapling:
```bash
bun run setup:py:paperqa   # Scrapling is installed in the PaperQA venv
```
And set `MEDSCI_PYTHON` for `medsci-acquisition` in `opencode.json` to `packages/server-paperqa/.venv-paperqa/bin/python3` (it already is by default).

### Sandbox tools fail with `docker: command not found` or connection errors
The sandbox tools require Docker Desktop 4.40+ with the AI Sandbox feature enabled. If Docker Desktop isn't installed or the daemon isn't running, sandbox calls return errors — all other tools continue to work normally.

### ACE MCP fails to start
Verify the PaperQA venv is set up (`bun run setup:py:paperqa`) and that `OPENROUTER_API_KEY` is exported before starting OpenCode (ACE uses OpenRouter by default).

## Project Structure

```
medsci-agent/
  packages/
    core/               Shared library (Ollama client, Python sidecar, config, types)
      python/
        sidecar.py      Long-running Python process with scientific library handlers
    server-drug/        Drug discovery MCP server
    server-protein/     Protein analysis MCP server
    server-literature/  Literature search MCP server
    server-acquisition/ Policy-controlled retrieval MCP server
    server-imaging/     Medical imaging MCP server
    server-omics/       Single-cell and omics MCP server
    server-paperqa/     Deep literature synthesis MCP server (identifier or document ingestion)
    server-sandbox/     Isolated sandbox execution MCP server
  .opencode/
    agents/             Agent definitions (orchestrator + 4 domain specialists + PaperQA routing)
    commands/           Reusable slash commands for MedSci workflows
    plugins/            OpenCode plugin guardrails and telemetry hooks
    skills/             Skill definitions for OpenCode
  opencode.json         OpenCode configuration (model, MCP servers)
```

---

## Runtime Artifacts

Sandbox runs generate runtime artifacts (for debugging and reproducibility), typically under `sandbox-artifacts/` or a configured artifact root:

- `job-*/stdout.log`
- `job-*/stderr.log`
- `job-*/metadata.json`

These are not source files and are safe to delete. Sandbox teardown removes containers; host-side artifacts remain unless explicitly pruned.

---

## Acknowledgments

This project builds on the following work:

- **Prompt Repetition** ([Leviathan, Kalman & Matias, 2025](https://arxiv.org/abs/2512.14982)) — Our `interpretWithMedGemma` function repeats the instruction after the data context to improve non-reasoning model accuracy.
- **TxGemma** ([Wang, Schmidgall, Jaeger et al., 2025](https://arxiv.org/abs/2504.06196)) — ADMET prediction uses verbatim prompt templates from Google's TxGemma, trained on [Therapeutics Data Commons](https://tdcommons.ai) benchmarks.
- **PaperQA2** ([Future-House/paper-qa](https://github.com/Future-House/paper-qa)) — Deep literature synthesis and RAG is powered by FutureHouse's PaperQA2 library, with text acquired via NCBI's BioC API.
- **Agentic Context Engine (ACE)** ([kayba-ai/agentic-context-engine](https://github.com/kayba-ai/agentic-context-engine)) — ACE MCP integration powers MedSci's strategy-learning and post-run self-improvement loop.
- **K-Dense Scientific Skills** ([K-Dense-AI/claude-scientific-skills](https://github.com/K-Dense-AI/claude-scientific-skills)) — The OpenCode skills in this project are adapted from K-Dense AI's open-source collection of 147+ scientific skills for AI agents.

---

## License

[MIT](LICENSE)

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