# How to integrate Synthesize Bio MCP with Atomic Agent

```json
{
  "title": "How to integrate Synthesize Bio MCP with Atomic Agent",
  "toolkit": "Synthesize Bio MCP",
  "toolkit_slug": "synthesize_bio_mcp",
  "framework": "Atomic Agent",
  "framework_slug": "atomic-agent",
  "url": "https://composio.dev/toolkits/synthesize_bio_mcp/framework/atomic-agent",
  "markdown_url": "https://composio.dev/toolkits/synthesize_bio_mcp/framework/atomic-agent.md",
  "updated_at": "2026-09-07T05:35:53.750Z"
}
```

## Introduction

Atomic Agent is an open-source AI agent that runs on your machine and supports local models through llama.cpp. Connect it to 1,500+ apps through Composio, including Synthesize Bio.
This guide uses Atomic Agent's built-in Composio integration. You need Atomic Agent v0.5.6 or later, your own Composio API key, and a Synthesize Bio account. See the [Atomic Agent documentation](https://atomicagent.io/docs/?cta_placement=atomic-agent-docs) for installation instructions.

## Also integrate Synthesize Bio MCP with

- [ChatGPT](https://composio.dev/toolkits/synthesize_bio_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/synthesize_bio_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/synthesize_bio_mcp/framework/hermes-agent)

## TL;DR

### How Atomic Agent connects to Synthesize Bio
Atomic Agent connects to Composio's Tool Router over Streamable HTTP MCP. It discovers the tools needed for your request, and Composio handles account authentication.
Execution and account-connection tools follow Atomic Agent's configured approval policy. Review any approval prompt before allowing an action on your connected account.

## Connect Synthesize Bio MCP to Atomic Agent

### Connect Synthesize Bio to Atomic Agent
- Sign up or sign in to the [Composio dashboard](https://dashboard.composio.dev/?cta_placement=atomic-agent-api-key). Copy your API key.
- In Atomic Agent, open the Integrations tab and select Composio. Select API key, press e, paste the key, and press Enter. The tools become available immediately, without a restart.
- Ask Atomic Agent to do something in Synthesize Bio. It searches Composio for the right tool.
- On first use, open the sign-in link returned in the chat. Connect your Synthesize Bio account, then return to Atomic Agent to continue.
### Headless setup
Add the following line to ~/.atomic-agent/.env, replacing YOUR_COMPOSIO_API_KEY with your key. Start Atomic Agent after saving the file.

```bash
COMPOSIO_API_KEY=YOUR_COMPOSIO_API_KEY
```

## What is the Synthesize Bio MCP server, and what's possible with it?

The Synthesize Bio MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your Synthesize Bio account. It provides structured and secure access so your agent can perform Synthesize Bio operations on your behalf.

## Supported Tools

| Tool slug | Name | Description |
|---|---|---|
| `SYNTHESIZE_BIO_MCP_ANALYZE_GENE_EXPRESSION` | Analyze gene expression | Starts a differential gene expression analysis using Synthesize Bio's AI platform. Requires the resolution_id returned by resolve_sample_metadata; raw natural-language prompts are not accepted. Requires `user_confirmed_metadata: true`. When the flag is missing or false, the call is rejected with failure_kind `user_confirmation_required`. Optional workspace_id selects which workspace owns the generated dataset. When omitted, the workspace from resolve_sample_metadata is used automatically. When the account has more than one workspace and the resolution has no workspace, the call is rejected with failure_kind `workspace_selection_required` and a `workspaces` list of `{ name, workspace_id }`. Returns a job_id immediately; get_analysis_results accepts that job_id and returns analysis status or results. The pipeline runs two steps: (1) GEM-1 — Synthesize Bio's Gene Expression Model inference; (2) Differential expression — GPU-accelerated DESeq2 (negative-binomial GLM with Wald test, Cook's outlier filter, and Benjamini-Hochberg padj). All genes are tested; pre-filtering is handled by DESeq2's independent filtering. If the query is unsupported, later polling responses include failure_kind `unsupported_query` and suggested_queries. Quota and monthly-limit errors include a request-higher-limits URL; a previous successful resolve does not grant an extra run when the account is out of budget. |
| `SYNTHESIZE_BIO_MCP_GET_ANALYSIS_RESULTS` | Get analysis results | Polls the status of a gene expression analysis. Each call waits server-side for a short bounded window and may return earlier if progress is detected. Responses always include a `structuredContent` object (declared by the tool's `outputSchema`); MCP clients read from `structuredContent` directly rather than re-parsing JSON out of the human-readable text. `structuredContent` always has `status` (one of `running`, `complete`, `failed`), `job_id`, and `steps_completed`. While running, it also has `step` (`gem_model` or `diff_expr`), `message`, and `progress_label`/`progress_percent`/`progress_bar`. Failed responses include `error`, and may also include `failure_kind`, `user_action_required`, and `suggested_queries`. When `status` is `complete`, `structuredContent` carries: `metadata` (prompt, modality, groups, plus summary counts such as `significant_genes`, `significant_up`, `significant_down`, `total_genes_tested`); `results` — up to 1000 differential expression rows (each with `gene_id`, `gene_symbol`, `log2FoldChange`, `pvalue`, `padj`, `neg_log10_padj` (pre-computed `-log10(padj)`, clamped to 300 if padj underflows), `direction`, `significant`) suitable for downstream analysis or visualization (e.g. a volcano plot with x = `log2FoldChange`, y = `neg_log10_padj`); `plot_results` — the top ~200 most significant rows (same per-row shape, pre-sorted most-significant-first), pre-sliced for charting; the full `results` array is better suited to tables, summaries, and analysis; `results_returned` and `results_total` for truncation accounting; `plot_results_returned` for the plotted subset size; `dataset_link` — `{ dataset_id, title, url }` for the Synthesize Bio platform dataset (or `null`). The accompanying `content[0].text` is a human-readable Markdown summary of the same data. For hosts that do not surface `structuredContent` (e.g. claude.ai), it inlines only the top ~200 most significant rows as an array of objects under a top-level `results` key — same per-row schema as `structuredContent.results`, including the pre-computed `neg_log10_padj` field — so chart-widget code can use those rows directly. The full result set remains available via `structuredContent.results` and the dataset link when present. |
| `SYNTHESIZE_BIO_MCP_GET_COUNTS_DATA_URL` | Get counts data url | Returns a presigned S3 URL to download the raw gene expression counts data (JSON) produced by a completed or in-progress analysis job. The data is typically large (20,000+ genes by N samples) and requires an environment with direct network access. The JSON has the following structure: { gene_order: string[] (Ensembl IDs), outputs: [{ counts: number[], metadata: object }], model_version: string }. Each entry in 'outputs' corresponds to one sample; 'counts' is aligned with 'gene_order'. The response also returns a second presigned URL to a small (~500 KB) Parquet file mapping every Ensembl `gene_id` in `gene_order` to its HGNC gene_name — both files join on gene_id to label genes by symbol. Both URLs expire after 1 hour; fresh responses contain fresh URLs. Available after analyze_gene_expression has completed the GEM-1 step. |
| `SYNTHESIZE_BIO_MCP_GET_METADATA_SCHEMA` | Get metadata schema | Returns the structured-metadata schema used to turn a natural-language experiment description into sample groups. Response fields include `group_schema` (the JSON shape of one sample group), the `fields` and `perturbation_fields` inventory for the active metadata version, and `instructions` for building the `groups` array. The resulting `groups` array is the input to resolve_sample_metadata. This tool makes no AI calls and consumes no usage budget. |
| `SYNTHESIZE_BIO_MCP_RESOLVE_SAMPLE_METADATA` | Resolve sample metadata | Deterministically harmonizes already-structured sample `groups` to Synthesize Bio's controlled ontology vocabulary. Does not accept a natural-language prompt and makes no AI calls. Input: `groups` — a JSON array of sample-group objects matching get_metadata_schema's `group_schema`. Returns a resolution_id and a per-group breakdown including tissue, disease, cell type/line (with resolved ontology ids), sex, age, and full perturbation details (type, label/id, gene mechanism and mechanism type, dose, dose count, timepoint). Each resolved field also carries ranked candidate options for disambiguation. If a value resolves to the wrong id, correcting the term in `groups` and calling again produces a new resolution. The `warnings` array flags issues such as a described drug that did not match the ontology. When status is `resolving`, the same resolution_id identifies the pending request and can be passed again to poll. A completed resolution_id is required by analyze_gene_expression. Optional workspace_id selects which workspace the resolution is stored under. When omitted, a single-workspace account is assigned automatically. When the account has more than one workspace and workspace_id is omitted, the call is rejected with failure_kind `workspace_selection_required` and a `workspaces` list of `{ name, workspace_id }`; no metadata resolution runs until the user picks and the tool is retried with workspace_id. Quota and monthly-limit errors include a request-higher-limits URL and indicate remaining samples/cells when available. |

## Supported Triggers

None listed.

## Troubleshooting

### Why is my API key rejected?

Copy the key directly from the Composio dashboard. Atomic Agent requires ASCII characters because it sends the key in an HTTP header. Remove any extra characters introduced when copying.

### Why are Composio tools unavailable after saving a key?

Check that you use Atomic Agent v0.5.6 or later and that Composio is enabled in your configuration. A "composio": { "enabled": false } setting disables the integration while keeping the saved key on disk.

### Does Composio have a free plan?

The Hobby plan includes 100,000 tool calls per month. Composio-managed OAuth apps have a lower included allowance. See [Composio pricing](/pricing) for the current limits that apply to your connection.

## Complete Code

None listed.

## Conclusion

### Use Synthesize Bio from Atomic Agent
With your account connected, ask Atomic Agent to work with Synthesize Bio in natural language. You can connect more apps through the same Composio integration as you need them.
Visit the [Atomic Agent website](https://atomicagent.io/?cta_placement=atomic-agent-site) or inspect the [Atomic Agent source code](https://github.com/AtomicBot-ai/atomic-agent?cta_placement=atomic-agent-repo).

## How to build Synthesize Bio MCP Agent with another framework

- [ChatGPT](https://composio.dev/toolkits/synthesize_bio_mcp/framework/chatgpt)
- [Claude Cowork](https://composio.dev/toolkits/synthesize_bio_mcp/framework/claude-cowork)
- [Hermes](https://composio.dev/toolkits/synthesize_bio_mcp/framework/hermes-agent)

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## Frequently Asked Questions

### What are the differences in Tool Router MCP and Synthesize Bio MCP?

With a standalone Synthesize Bio MCP server, the agents and LLMs can only access a fixed set of Synthesize Bio tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Synthesize Bio and many other apps based on the task at hand, all through a single MCP endpoint.

### Can I use Tool Router MCP with Atomic Agent?

Yes, you can. Atomic Agent fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right Synthesize Bio tools.

### Can I manage the permissions and scopes for Synthesize Bio while using Tool Router?

Yes, absolutely. You can configure which Synthesize Bio scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

### How safe is my data with Composio Tool Router?

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your Synthesize Bio data and credentials are handled as safely as possible.

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