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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.

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

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Mention Categories

When you type @, the dropdown organizes resources into tabs:
TabContainsExamples
AllEverything availableAll resources and files
FilesYour uploaded files and results@sample.fastq, @results.csv
DatabasesReference databases@UniProt, @NCBI, @PDB
ToolsAnalysis software@STAR, @GATK, @AlphaFold
PackagesR/Python libraries@DESeq2, @Seurat, @pandas

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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”

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Keyboard Navigation

KeyAction
↑ ↓Move selection
Tab or EnterConfirm selection
EscClose without selecting
TypeFilter results

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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

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