AI research assistant: ask your files and the literature

Biocompile’s AI research assistant is an AI co-scientist that answers questions about your files and the literature, runs analyses as Python and R code in a private sandbox, and proposes changes to your projects as contributions. The Biocompile homepage calls it the AI co-scientist. Everything it produces stays in the conversation until it is contributed to a project.

What the assistant can do

Search the literature in PubMed, arXiv, bioRxiv, OpenAlex and Semantic Scholar, search patents by class, applicant and country, query public biological databases, and cite every source it uses.
Read files from your Knowledge Atlas when you mention them.
Write and run analysis code in an isolated sandbox with Python, R and Bioconductor, and show you the code it ran.
Create files such as tables, figures and notes that you can reuse later.
Pick up earlier work in the same conversation and build on it.

Work in a conversation

A conversation with the assistant opens in the assistant pane. If the pane is hidden, choose Show assistant in the top bar, then choose New conversation. Conversations in the sidebar lists every conversation with its project and last activity.

Ask a focused question and name the files that matter. In the message box, type @ to reference a file, or drag or paste a file to attach it. The assistant works in visible Work steps: open a step to see its Request and Response, including the code it ran.

The send button stays disabled until the message has text or an attachment. When a selection you made answers the assistant, a note says it is ready and asks you to press Send.

Fit a logistic growth model to each well in plate_reader_OD600_2026-03.csv and flag wells whose curves suggest contamination.

Each conversation has a Conversation workbench that collects what the assistant produced: proposed project changes, the files and sandboxes it used, the research material it found, and its activity.

If a sandbox does not start

When the sandbox cannot start, a Sandbox could not start notice explains why and what to do:

Cause	What the notice tells you
Quota	Your sandbox resource quota is full. Stop unused sandboxes or ask your administrator to review your quota.
Capacity	Sandbox resources are busy. Wait a moment, then try again.
Timeout	The sandbox did not start in time. Try again, and contact support if it continues.
Recovery	The sandbox could not be recovered safely. Contact support before you try to restore it again.

Except for a recovery problem, the notice offers Try starting again.

Link a conversation to a project

A conversation works with one project. Under the message box, open No project and select a project under Project context. The first selection binds the conversation to that project for good, and so does the first change the assistant proposes to one. Start a new conversation to work with a different project.

Selecting a project gives the assistant its context and fixes where proposed work will go. It does not add anything to the project by itself. A project whose agent change policy is Read only can still provide context, but cannot receive contributions.

Choose the model

The assistant’s model comes from the agent profile you choose beside the message box (Choose co-scientist). Each profile has a default model family, set under Agents → Agent Profiles. Within that family, Choose intelligence sets the model size and thinking for the conversation. The agent profile is fixed once a conversation has started, so start a new conversation to use another profile.

Your organization’s security policy decides which models you may use. A model it does not allow is marked “Blocked by organization policy”. See When a model is blocked.

Contribute conversation work

A contribution is the reviewed set of changes through which work from a Biocompile conversation reaches a project. Changes the assistant proposes are provisional: they stay in the conversation’s Contribution draft until they are contributed and accepted. Hovering over Contribute work shows How contributions work, a summary of the flow.

Choose Contribute work under the message box. When the assistant asks “Contribute this work?”, choose Contribute work, or Not now to decline.
If the conversation is not bound to a project yet, choose one under Choose a project, then choose Prepare contribution. Result: the conversation shows “Preparing contribution” while Biocompile collects the durable findings into proposed changes, and the message input is paused.
Review the contribution: its summary, every proposed change as a before-and-after comparison, and the evidence behind each one. You can edit proposed values; your edits are saved as a new revision, and the version you reviewed first stays in the history.
Choose Accept contribution. Result: Biocompile shows “Contribution approved and applied”, and the changes appear in the project.

The same review is available on the project’s Contributions tab. Only accepting a contribution changes the project; proposing and preparing never do.

Request a revision

Choose Revise, describe what should change under Revision instructions, and choose Request revision. Choose Withdraw to drop your own contribution, or Decline for someone else’s.

When a contribution cannot be applied

A conflicted contribution applies nothing, and the review names the reason:

A project rule prevented this contribution. The change would break a rule of the project, such as two records with the same name. Revise the proposed changes and submit them again.
The project changed before approval. A value the contribution relied on changed after the contribution was prepared. Choose Revise conflicts and revise the proposed changes using the conflict details.

Auto Mode

Auto Mode sits beside the message box. It lets the assistant answer the approval checkpoints you select for it under What Auto Mode handles for you in Settings → Assistant. With Contributions selected there, it prepares and applies contributions without asking. With Auto Mode off (Contribute Mode), every contribution waits for your review.

An organization admin can pin a category for everyone under Organization → Policies, for example Always review. Demo and regulated (GxP) organizations cannot use Auto Mode.

Common questions

Can the assistant change my project without my approval?

Only if you allow it. In Contribute Mode, nothing the assistant proposes reaches a project until someone chooses Accept contribution. In Auto Mode with Contributions selected, the assistant applies contributions itself. To review each one, turn Auto Mode off in the conversation, or ask an admin to set contributions to Always review. A project whose agent change policy is Read only never receives contributions.

Which AI models can I use in Biocompile?

Biocompile offers Claude and GPT models and open models such as Qwen, DeepSeek and GLM, in model families with smaller and larger members. Some families process data in the EU. The agent profile you choose sets the family, and your organization’s security policy decides which models are available.

Does the assistant show the code it ran?

Yes. Each step of the assistant’s work shows its request and response, so you can read the code behind every result.