> ## 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.

# @ Mention System

> Reference files, databases, and tools in your requests

Type `@` in the chat input to reference specific resources in your request.

## Mention Categories

When you type `@`, the dropdown organizes resources into tabs:

| Tab           | Contains                        | Examples                    |
| ------------- | ------------------------------- | --------------------------- |
| **All**       | Everything available            | All resources and files     |
| **Files**     | Your uploaded files and results | @sample.fastq, @results.csv |
| **Databases** | Reference databases             | @UniProt, @NCBI, @PDB       |
| **Tools**     | Analysis software               | @STAR, @GATK, @AlphaFold    |
| **Packages**  | R/Python libraries              | @DESeq2, @Seurat, @pandas   |

## Search and Filtering

The mention search uses fuzzy matching—you don't need exact names:

* `@deseq` matches **DESeq2**
* `@uniprot` matches **UniProt**
* `@sample` matches all files containing "sample"

### Keyboard Navigation

| Key              | Action                  |
| ---------------- | ----------------------- |
| `↑` `↓`          | Move selection          |
| `Tab` or `Enter` | Confirm selection       |
| `Esc`            | Close without selecting |
| Type             | Filter results          |

## Multiple Mentions

Chain resources in a single request:

```
Align @sample_R1.fastq.gz and @sample_R2.fastq.gz using @STAR,
quantify with @featureCounts, then run differential expression
with @DESeq2 comparing treatment vs control
```

## File Mentions

Reference files you've uploaded:

```
Analyze @experiment_data.csv
```

Reference output from previous analyses:

```
Using the @aligned_reads.bam from earlier, call variants with @GATK
```

<Tip>
  Mentions are optional. Biomni can often infer the right tools from context—use @ when you want a specific resource.
</Tip>