> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biomni.phylo.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# How to Prompt

> Give Biomni a clear scientific goal, the right inputs, and useful constraints

You do not need to write a formal protocol before starting. A strong request
makes the scientific goal and evidence boundary clear, then lets Biomni plan the
implementation.

## Start with the outcome

Say what you need to learn, decide, or deliver.

<Tabs>
  <Tab title="Too broad">
    ```text theme={null}
    Analyze my data.
    ```
  </Tab>

  <Tab title="Actionable">
    ```text theme={null}
    Identify genes that differ between treatment and control in @counts.csv,
    then create a ranked result table and a publication-ready volcano plot.
    ```
  </Tab>
</Tabs>

## Include the experimental context

Add details that change the interpretation or method:

* organism, reference build, assay, and tissue or cell type;
* cohort definitions, controls, replicates, and batch structure;
* units, column meanings, and missing-value conventions;
* primary endpoint or research question; and
* whether the work is exploratory, confirmatory, or intended for publication.

```text theme={null}
These are paired tumor and adjacent-normal RNA-seq samples from 12 patients.
Patient ID is the blocking variable in @metadata.csv. Use GRCh38 annotations and
report both effect size and adjusted p-value.
```

## Attach or mention the evidence

Use **+ Add** for files, folders, cloud imports, Skills, resources, and
connectors. Type `@` to search files and scientific resources, or `+` to search
Skills.

Do not rely on a filename alone when its structure is ambiguous. Explain which
sheet, columns, groups, or identifiers matter.

## State constraints without over-specifying

Specify a method when it is scientifically required. Otherwise, state the
constraint and ask Biomni to choose and justify the method.

```text theme={null}
Use a method appropriate for paired count data. Before running it, explain the
design formula, filtering rule, and multiple-testing correction you chose.
```

Useful constraints include:

* required or prohibited methods;
* quality thresholds and inclusion criteria;
* resource or runtime limits;
* databases or date ranges to search;
* output format, dimensions, and naming; and
* citation or reproducibility requirements.

## Ask for inspectable outputs

Request the artifacts needed to audit or continue the work:

```text theme={null}
Return the full result table as CSV, the analysis notebook, SVG and PNG versions
of each figure, and a short README describing inputs, software, parameters, and
output files.
```

For literature or database research, ask for linked sources next to the claims
they support. For data analysis, ask Biomni to separate observed results from
interpretation.

## Use follow-up turns

Keep related refinement in the same task so Biomni can use the conversation and
generated files.

```text theme={null}
The plot is correct, but label only the ten genes with the smallest adjusted
p-values and increase the axis-label size. Do not rerun the statistical model.
```

If the goal changes substantially, start a new task. This keeps the evidence,
assumptions, and results for each analysis easier to review.

## When you are unsure

Ask Biomni to identify missing information before it acts:

```text theme={null}
I want to test changes across three timepoints in this RNA-seq experiment. Read
@metadata.csv and tell me what design details you still need before choosing a
model. Do not run the analysis yet.
```

For high-impact conclusions, finish with an explicit verification request and
run [Scientific Review](/features/scientific-review).