Research projects: hypotheses, evidence and decisions

A Biocompile project is the home of one line of research: its questions, hypotheses, evidence, plans and decisions, next to the files and results that produced them. Because the reasoning lives beside its evidence, you and your colleagues can come back months later and see why a direction was chosen and what was already ruled out.

Create a project

Open Research Projects to see your projects and filter them by status.

Choose New Project.
Enter a Project Name, and optionally the Motivation and a Description.
Under Advanced, choose the Status (Draft or Active), the Agent change policy and the Visibility, and whether to Keep this project up to date.
Choose Create Research Project. Result: Biocompile shows “Project created” and opens the new project.

Agent change policy decides how the assistant may change the project:

Review before apply keeps its changes in a contribution until a person accepts them.
Read only lets the assistant use the project as context but never change it.

Inside a project

Each project opens in a tabbed workspace. Select a tab to move between areas of the project. Each tab loads its content on first visit and stays loaded while you navigate.

Tab	What it holds
Overview	A written summary of the project’s purpose, current position and most important open question, with links to the records it cites.
Knowledge	The research material and references the project draws on, and its Reports.
Laboratory	Experiments, lab work and compute runs recorded against the project.
Reasoning	Hypotheses, observations and the evidence that connects them.
Progress	Plans, tracks and tasks, and what is blocking them.
Contributions	Changes proposed to the project, waiting for review or already applied.
Comments	Threaded discussion about the project.
History	An audit trail of everything that changed, and who changed it.

Project overview

The project overview is written for you from the project’s records and updated as the project changes. Each claim links to the record it comes from, and a table under the summary lists every cited source with the area of the project it belongs to. When recent changes are not reflected yet, the overview says so.

Reasoning: hypotheses and evidence

Reasoning shows how observations bear on hypotheses. Every link between an observation and a hypothesis is an evidence assessment with one of four relations:

Relation	Meaning
Supports	The observation makes the hypothesis more likely.
Contradicts	The observation counts against the hypothesis.
Qualifies	The observation limits where or how the hypothesis holds.
Inconclusive for	The observation was considered and does not decide the question.

Use Propose Hypothesis and Record Observation to add records directly. Items that need a person’s decision collect under Review, with a Queue of open items and a History of past decisions.

Progress: plans, tracks and tasks

Progress organizes the work: plans group tracks, and tracks group tasks. Expand a row to see its details and edit it in place. Open Blockers to see what is holding work up.

Contributions to a project

Work from a conversation reaches a project as a contribution, which someone accepts or sends back for revision on the Contributions tab. The full flow is under Contribute conversation work.

Archive a project

To archive a project from the project list, open its row actions and select Archive project. Archived projects remain visible when you filter by the Archived status.

Keep a project easy to return to

Give the project a specific title, such as “Xylose uptake in strain K12-04”.
Record decisions and dead ends as you make them, not at the end.
Keep raw and processed data apart in the Knowledge Atlas.

Common questions

Who can see a project?

Everyone in your organization, unless you select teams under Visibility when you create the project. Then only members of those teams see it. An organization can require every project to be visible to at least one team.

Can I stop the assistant from changing a project?

Yes. Choose Read only as the Agent change policy when you create the project. The assistant can still use the project as context, but it cannot receive contributions.

Can Biocompile watch a project for new papers?

Yes. With Keep this project up to date on, the agent looks for new papers and next steps once a week and emails you when it finds something.