# How to connect Synthesize Bio to Grok Bot

```json
{
  "title": "How to connect Synthesize Bio to Grok Bot",
  "toolkit": "Synthesize Bio MCP",
  "toolkit_slug": "synthesize_bio_mcp",
  "framework": "Grok Bot",
  "framework_slug": "grok-bot",
  "url": "https://composio.dev/toolkits/synthesize_bio_mcp/framework/grok-bot",
  "markdown_url": "https://composio.dev/toolkits/synthesize_bio_mcp/framework/grok-bot.md",
  "updated_at": "2026-11-09T06:01:34.314Z"
}
```

## Introduction

Grok is xAI's assistant, and its bot builder lets you create a personal agent that holds context, runs skills, and connects to the apps you already use through plugins.
This guide explains how to connect Synthesize Bio to a Grok bot using Composio Connect, which handles OAuth, token refresh, and reliability so you do not have to. You add Composio as a plugin, authenticate once, then ask your bot to work with Synthesize Bio in plain language.

## 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)
- [Atomic Agent](https://composio.dev/toolkits/synthesize_bio_mcp/framework/atomic-agent)

## TL;DR

Composio exposes 1,500+ apps to your Grok bot through a single connection, so you get:
- Connect to 1,500+ apps with on-demand tool loading, so you do not fill your context window with unnecessary tool definitions.
- Use programmatic tool calling through a remote workbench, letting the model write its own code to handle complex tool chaining. This reduces back-and-forth for frequent tool calls.
- Handle large tool responses outside the model context to keep conversations lean.

## Connect Synthesize Bio MCP to Grok Bot

### Connecting Synthesize Bio to Grok Bot
Once Grok Bot is set up, you connect Synthesize Bio entirely from its interface, and the whole flow takes under a minute.
### Set up Grok Bot
Get access. Grok Bot is included with Cursor Ultra, Cursor Premium Teams, and SuperGrok Heavy. Get the desktop app for macOS or Windows from [x.ai/bot](https://x.ai/bot) and sign in. An iPhone companion app is also available, and your bots sync across devices.
Create a bot. Pick a suggested role or define your own, then give it a short name, one primary job, and a short description of how it should work. Focused bots work best, because a clear role gives the bot more useful context over time.
### Connect Synthesize Bio
### 1. Add the Composio plugin
Click the button. The Composio listing on x.ai opens and launches Grok Bot for you. If the app does not open on its own, click Add to Grok Bot.
[Add to Grok Bot](https://x.ai/bot/plugin/32661537)
Grok Bot opens the Composio plugin, showing its connector and skills. Click Add.
### 2. Authenticate
Go to the Installed section and click the Composio entry. You'll see its connector and skills listed.
Click Authenticate. You'll be taken to the Composio consent screen. Review the access it requests and click Authorize. Composio handles the OAuth handshake for you, so you never touch API keys or tokens.
### 3. Connect your Synthesize Bio account
Back in the chat, ask your bot to connect to Synthesize Bio or give it any Synthesize Bio task.
For example, ask it to:
- "Run differential expression on latest samples"
- "Start single-cell pipeline for patient sample"
- "Fetch results and generate QC summary report"
It will prompt you to authenticate and authorize access.
That's it. Composio's tools are now available in your Grok bot, and your Synthesize Bio account is ready to use.

## What is Grok Bot?

Grok is xAI's assistant, available as a chat interface and a bot builder for creating personal agents that run skills and connect to external apps.
With Composio Connect, your Grok bot can securely access apps like Synthesize Bio through MCP without you sharing account credentials directly with the agent.

## 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 to gene-expression analyses, results, counts data, and sample metadata, so your agent can start analyses, monitor progress, retrieve results, access counts data, and harmonize sample metadata on your behalf.
- Gene-expression analysis: Have your agent start a differential gene-expression analysis using your experiment data.
- Analysis monitoring: Let the agent check the status of an analysis and retrieve its results when available.
- Counts data access: Direct your agent to access the raw gene-expression counts data produced by an analysis.
- Metadata schema retrieval: Instruct your agent to retrieve the structured metadata schema used to organize samples into groups.
- Sample metadata harmonization: Have your agent map structured sample groups to Synthesize Bio's controlled ontology vocabulary.

## 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.

## Creating MCP Server - Stand-alone vs Composio SDK

Once connected, your Grok bot can access the Synthesize Bio MCP server through Composio to run the actions you authorize, using plain language in the chat.

## Complete Code

None listed.

## Conclusion

### Way Forward
Now that Synthesize Bio is connected, extend your setup by connecting the other apps you already use every day, so your Grok bot can run true cross-app workflows end to end.
- Connect Calendar to turn threads into scheduled meetings automatically.
- Connect Slack or Teams to post summaries, approvals, and alerts where your team works.
- Connect Notion, Linear, Jira, or Asana to convert requests into tickets, tasks, and docs.
- Connect Drive, Dropbox, or OneDrive to fetch, file, and share attachments without manual steps.
Start with one workflow you do repeatedly, then keep adding apps as you find new handoffs. With everything behind a single connection, your bot can coordinate multiple tools safely and reliably in one conversation.

## 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)
- [Atomic Agent](https://composio.dev/toolkits/synthesize_bio_mcp/framework/atomic-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 Grok Bot?

Yes, you can. Grok Bot 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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