---
title: "Research projects: hypotheses, evidence and decisions"
description: "Organize a line of research as a Biocompile project, with hypotheses and the evidence for and against them, experiments, plans, reports and contributions."
url: https://www.biocompile.com/docs/projects/
section: "Projects and assistant"
last_updated: 2026-10-23
app_url: https://app.biocompile.com/research-hub
---

# Research projects: hypotheses, evidence and decisions

> Organize a line of research as a Biocompile project, with hypotheses and the evidence for and against them, experiments, plans, reports and contributions.

Source: https://www.biocompile.com/docs/projects/. Index of all Biocompile documentation: https://www.biocompile.com/docs/index.md

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.

1. Choose **New Project**.
2. Enter a **Project Name**, and optionally the **Motivation** and a **Description**.
3. Under **Advanced**, choose the **Status** (**Draft** or **Active**), the
   **Agent change policy** and the **Visibility**, and whether to
   **Keep this project up to date**.
4. 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](https://www.biocompile.com/docs/ai-research-assistant.md#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.

## Related

- [AI research assistant: ask your files and the literature](https://www.biocompile.com/docs/ai-research-assistant.md)
- [Research reports: save cited findings and build on them](https://www.biocompile.com/docs/research-reports.md)
- [Knowledge Atlas: upload, preview and edit lab files](https://www.biocompile.com/docs/knowledge-atlas.md)

## Get access to Biocompile

Biocompile is used in the browser at https://app.biocompile.com. It is free to start and no payment method is required: sign up at https://app.biocompile.com/signup?mc_cta=docs-md&mc_path=/docs/projects.md. If your team already uses Biocompile, ask an organization admin to invite you. Research teams that want hands-on setup can apply for the founder-led pilot at https://www.biocompile.com/pilot/. Questions: https://www.biocompile.com/contact/.