How to Prompt

Getting the best results from Biomni Lab starts with clear communication. This guide covers how to write effective prompts that help Biomni Lab understand exactly what you need.

Basic Principles

Be Specific

The more specific your request, the better Biomni Lab can help.

Less Effective
More Effective

Analyze my data

Perform differential expression analysis on @rnaseq_counts.csv
comparing the treatment vs control groups, using DESeq2 with
an adjusted p-value cutoff of 0.05

Provide Context

Tell Biomni Lab about your research goals and any constraints.

I'm studying drug resistance in cancer cells. Analyze the mutation
data in @variants.vcf to identify potentially druggable targets.
Focus on genes in the MAPK signaling pathway.

Use @ Mentions

Reference your files and preferred tools directly:

Align @sample1_R1.fastq.gz and @sample1_R2.fastq.gz to the human
genome (GRCh38) using @STAR, then count reads per gene with @featureCounts

Examples

Check out the example prompts in the UI for inspiration on well-structured requests.

Tips for Better Results

Break Down Complex Tasks

Instead of one massive request, break it into logical steps:

Step 1: Quality Control

Run FastQC on @sample.fastq.gz and summarize the quality metrics

Step 2: Alignment

The QC looks good. Now align the reads to GRCh38 using STAR

Step 3: Analysis

Great, now count reads per gene and identify highly expressed genes

Specify Output Format

Tell Biomni Lab exactly what you want:

“Generate a heatmap showing…”
“Create a CSV file with columns for…”
“Output a summary report including…”
“Save the results as a PDF figure”

Include Relevant Parameters

If you have specific requirements, include them:

Align reads with the following parameters:
- Minimum mapping quality: 30
- Allow up to 2 mismatches
- Remove PCR duplicates
- Output sorted BAM file

Reference Previous Results

Build on earlier work in the conversation:

Using the differentially expressed genes from the previous analysis,
perform GO enrichment analysis focusing on biological processes

Iterating on Results

Biomni Lab learns from your feedback within a conversation:

Refining Results

The volcano plot looks good, but can you:
- Increase the font size for labels
- Highlight genes in the apoptosis pathway in red
- Add a title "Differential Expression: Treatment vs Control"

Correcting Course

Actually, I want to use edgeR instead of DESeq2 for this analysis
because my sample size is small

Asking for Alternatives

Can you show me a different visualization? Maybe a MA plot instead
of a volcano plot?

Getting Help

If Biomni Lab doesn’t understand your request:

Rephrase your prompt with more specific details
Break down complex requests into smaller steps
Provide examples of what you’re looking for
Ask Biomni Lab to explain what information it needs

I'm not sure how to phrase this - I have RNA-seq data from 3 timepoints
and want to find genes that change over time. What information do you
need from me to set up this analysis?

Get Started

Features

Support

Basic Principles

Be Specific

Provide Context

Use @ Mentions

Examples

Tips for Better Results

Break Down Complex Tasks

Specify Output Format

Include Relevant Parameters

Reference Previous Results

Iterating on Results

Refining Results

Correcting Course

Asking for Alternatives

Getting Help

​Basic Principles

​Be Specific

​Provide Context

​Use @ Mentions

​Examples

​Tips for Better Results

​Break Down Complex Tasks

​Specify Output Format

​Include Relevant Parameters

​Reference Previous Results

​Iterating on Results

​Refining Results

​Correcting Course

​Asking for Alternatives

​Getting Help

Basic Principles

Be Specific

Provide Context

Use @ Mentions

Examples

Tips for Better Results

Break Down Complex Tasks

Specify Output Format

Include Relevant Parameters

Reference Previous Results

Iterating on Results

Refining Results

Correcting Course

Asking for Alternatives

Getting Help