User guide · Connectors
Use BioMate with your AI assistant
Connect your account, find an analysis workflow, and work with your results from the assistant you already use.
What you can do
Ask your assistant to search BioMate workflows, help plan an analysis, start a run, check its progress, and explain the results. You can also search literature, look up public datasets, and export prepared findings.
You can make these requests in ordinary language. Your assistant uses the BioMate connector to carry them out.
Choose your app
The setup commands below are for Claude Code, Claude Desktop, Cursor, and Codex CLI. You will need a BioMate account, your chosen app, and Node.js 18 or later with npm installed.
For ChatGPT or a team messaging app, see Other integrations.
Connect your account
- Open Terminal on macOS or PowerShell on Windows.
- Copy and run the command for your app below.
- When your browser opens, sign in to BioMate and review the requested access.
- Return to your app and restart it to load the connector.
- Start a conversation and ask: “Search BioMate for RNA-seq differential expression workflows.”
If your app asks whether BioMate may use a tool, review the request and allow it to continue.
Claude Code
npx @biomate/connect@0.1.1 claude-codeFollow the browser sign-in prompts, then restart Claude Code.
Claude Desktop
npx @biomate/connect@0.1.1 claude-desktopFollow the browser sign-in prompts, then restart Claude Desktop.
Cursor
npx @biomate/connect@0.1.1 cursorFollow the browser sign-in prompts, then restart Cursor.
Codex CLI
npx @biomate/connect@0.1.1 codexFollow the browser sign-in prompts, then restart Codex CLI.
Run your first analysis
1. Find a suitable workflow
Search BioMate for RNA-seq differential expression workflows.Review the suggested workflows. Ask your assistant to explain the required inputs and help choose an approach for your study.
2. Prepare the inputs
Show me the required inputs for the workflow I selected.
Help me check my sample groups and analysis settings before starting.Provide files or data locations that BioMate can access. For RNA-seq, confirm the organism, reference, sample groups, biological replicates, and comparison you want to make.
3. Start the run
Start the selected workflow using the inputs and settings we reviewed.A suggested plan does not start an analysis. When you are ready, ask your assistant to submit it. Keep the run ID returned by BioMate so you can refer to the same analysis later.
4. Check progress
Check the status of my BioMate run.Each request retrieves the latest status. Ask again when you want an update; progress does not refresh continuously in the conversation.
5. Review the results
Show the output files and available findings for this run.
Explain the quality-control results before summarizing the biological findings.Check the quality-control results and supporting output files before drawing conclusions.
6. Export your findings
Export the findings for this run as Markdown.Markdown is a text format with headings and lists. You can open it in a compatible editor and revise it for your report. If BioMate says the findings are still being prepared, try again later.
Everyday requests
Replace the example topic with your own question. Include the run ID when referring to a specific analysis.
| Task | What to ask |
|---|---|
| Find a workflow | “Search BioMate for single-cell RNA-seq workflows.” |
| Plan an analysis | “Help me plan an analysis for this study. Ask me for any missing information.” |
| Find public data | “Look up this dataset accession and explain what data are available.” |
| Search literature | “Find publications about this research question and include the sources.” |
| Review previous work | “List my recent BioMate runs.” |
| Inspect outputs | “Show the output files for this run.” |
| Understand a failure | “Explain why this run failed and what I should check next.” |
| Cancel a run | “Cancel this BioMate run.” Include the run ID to identify it. |
| Export findings | “Export this run’s findings as Markdown.” |
Manage your connection
Use your own BioMate account when connecting. The connector keeps you signed in automatically. If you are asked to sign in again, rerun the setup command for your app and follow the browser prompts.
If you connected with an older installer, run the command above once to reconnect, then restart your app.
Your assistant receives the information you send and the results BioMate returns. Choose data that your organization permits you to use with that assistant.
Organization-managed setup
If your organization provides a BioMate connection or personal API key, follow your administrator’s instructions. Use an API key only in the app’s designated connection settings; do not paste it into a conversation.
ChatGPT
Setup for this app is separate from the commands above. Contact BioMate for availability and setup guidance for your account.
Slack
Setup for this app is separate from the commands above. Contact BioMate for availability and setup guidance for your account.
Feishu / Lark
Setup for this app is separate from the commands above. Contact BioMate for availability and setup guidance for your account.
Troubleshooting and questions
BioMate does not appear in my app. What should I do?
Close and reopen your app after setup. If BioMate is still missing, rerun the command for that app and make sure browser sign-in completes.
The terminal says “npx” is not found.
Install Node.js 18 or later with npm, open a new terminal window, and run the setup command again.
Sign-in does not complete.
Rerun the setup command and complete sign-in in the browser window it opens. If your account requires multi-factor authentication, contact BioMate for help; this connector sign-in flow does not currently support it.
Why has the progress message not changed?
Progress is retrieved when you ask for it. Ask your assistant to check the run again using its run ID.
My run has finished. Why is the report pending?
Preparing findings can take additional time after the analysis finishes. Check again later and ask your assistant to export the findings once they are ready.
Can I export a PDF or Word document?
The connector exports prepared findings as Markdown. Open the exported text in a compatible editor if you need to format it for another document type.
How do I revise a report?
Export the Markdown findings and edit the text in your preferred editor. Asking your assistant to rewrite its answer does not save a revision to the report in BioMate.
Still need help? Contact BioMate support.