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Tips, Troubleshooting & FAQ

This page collects practical advice for working with OmicsBox in an AI assistant, solutions to common problems, and answers to frequent questions. To connect an assistant, see Connect Your AI Assistant.

Tips for better results

  • Name the analysis or the tool. A request such as "Run InterProScan" leads to the right tool faster than a general description. If you are not sure, ask "Which OmicsBox tool should I use to…?" first.
  • Point to the exact file. Give the file name and folder, for example "proteins.fasta in the Uploads folder". If a folder contains several similar files, ask the assistant to list them first.
  • Describe your experimental design. For analyses with conditions or groups, such as differential expression, tell the assistant which column or file contains the conditions and which groups to compare. You can also ask it to read the input file first and confirm the names it finds.
  • Review the parameters before long runs. Ask "Show me the parameters you will use" before the job starts. Changing a value before the run is faster and cheaper than running the analysis again.
  • Ask for the status later. Long jobs run in the background. There is no need to wait in the conversation. Ask for the status when you come back.
  • Keep the run ID. The assistant always reports a run ID. In a new conversation, give it the run ID to continue with the same job.
  • Ask for the OmicsBox Web links. Results are easier to explore in the Results viewer than in the conversation. Ask for the link to the report or to the output folder.
  • Use OmicsBox for charts and exports. OmicsBox includes charts and exports for many results. Ask the assistant to use them rather than to write its own code. The charts can then be opened and edited in OmicsBox Web.

Limits

  • Files must be in your cloud storage. The assistant cannot read files from your computer or from the conversation. Upload them to OmicsBox as described in Provide input files.
  • Assistants stop waiting after about 1 minute. Most assistants cancel a tool request that takes longer than about 60 seconds. For this reason, OmicsBox returns a run ID immediately and the job continues in the cloud.
  • Download links expire after 15 minutes. The links to the output folder and to open results in OmicsBox Web do not expire.
  • Repeated requests are combined. The same request submitted twice within 20 minutes returns the job that is already running.

Troubleshooting

The assistant does not show OmicsBox, or does not use it. Check that the connector is added and enabled. In Claude, connectors can be switched on and off for each conversation from the + menu. In ChatGPT, select OmicsBox in each new conversation from + > Developer mode. On Claude Team and Enterprise plans, an organization owner must add the connector first.

No sign-in page opens. Some assistants only start the sign-in when the connector is added. Remove OmicsBox from the assistant and add it again. In Codex, log in explicitly from the MCP settings, then restart Codex or open a new task.

The connection fails with "Connection not completed". The sign-in was cancelled or the request expired. Start the connection again from your assistant.

The assistant reports that your identity is unavailable. Your OmicsBox account has not been used in the cloud yet. Sign in once to OmicsBox Web or to the desktop application, then try again.

Jobs cannot be started because there is no active subscription. Analyses need an active subscription. Check your subscription in Settings > Subscription Details in OmicsBox Web. If you connected before your subscription was active, disconnect the assistant in Settings > Connected apps and connect it again to choose the subscription.

The upload link from the assistant does not work. Assistants that run in a browser or a desktop app usually cannot upload files themselves. Ask the assistant for the OmicsBox Web upload link, upload the file on the Files page, and then tell the assistant that the upload is done.

A download link does not open. Download links expire after 15 minutes. Ask the assistant for new links, or use the link to the output folder in OmicsBox Web.

The first request is slow or times out. The first request of a session can take up to about 30 seconds while the OmicsBox tools start. Repeat the request. In Claude Code, increase the timeout as described in Claude Code.

The job failed. Ask the assistant to show the logs of the run. The log messages usually explain the problem, for example an input in the wrong format or a missing parameter. You can also inspect the job in the Jobs page of OmicsBox Web.

If the problem persists, contact BioBam support as described in Technical Requirements and Support Services.

Frequently asked questions

Does connecting an AI assistant cost extra? No. The analyses the assistant starts use Cloud Units from your subscription in the same way as analyses launched from the desktop application. Most tools are included in the subscription. The cost of the AI assistant itself depends on your plan with its provider.

Which assistants can I use? Any assistant that supports remote MCP servers, also called custom connectors. This includes Claude, ChatGPT, Claude Code, Codex, Cursor, VS Code, and Windsurf. See Connect Your AI Assistant for the steps for each one.

Can my colleagues use my connection? No. Each person connects with their own OmicsBox account and approves the connection separately. Share results through OmicsBox cloud storage instead, as described in Share files.

Can I choose which subscription pays for the analyses? Yes. You choose the subscription on the approval page when you connect. To change it later, disconnect the assistant and connect it again.

How do I stop an assistant from using my account? Open Settings > Connected apps in OmicsBox Web and select Disconnect. The change takes effect immediately. If you connected with an Engine API key, revoke the key in Settings > Engine API Keys.

Does the AI provider use my data to train its models? This depends on the policy of the provider and on the settings of your plan with them. Your input files and results stay in your OmicsBox cloud storage. Check the privacy settings of your assistant for details.

What is MCP? The Model Context Protocol (MCP) is an open standard that lets AI assistants use external tools and services. OmicsBox provides an MCP server, which is what you add to your assistant as a connector. You do not need to know how it works to use it.