Usage Tips

Follow these tips to get the most out of your BIOS research sessions.

Be Specific

More specific questions yield better results:

Provide Context

Include relevant context in your questions:

• Disease area or biological system - "in the context of Alzheimer's disease"
• Specific genes, proteins, or pathways - "focusing on the mTOR pathway"
• Time frame for literature - "papers from the last 5 years"
• Analysis requirements - "use FDR < 0.05 for significance"
• Organism or model system - "in human cell lines" or "mouse models"

Use Iterative Refinement

Start broad and narrow down based on initial findings. BIOS excels at multi-iteration research where each cycle builds on previous discoveries.

Example workflow:

1. Start with a broad question: "What is known about drug X in disease Y?"
2. Review findings and identify interesting leads
3. Drill down: "Explore the mechanism of action through pathway Z"
4. Request data analysis: "Analyze the attached dataset for genes in pathway Z"

Choose the Right Mode

• Use Steering Mode when you have a specific hypothesis and want precise control
• Use Semi-Autonomous for exploratory research where you want to guide but not micromanage
• Use Fully Autonomous for comprehensive reviews or well-defined questions

Leverage Both Agents

BIOS is most powerful when combining literature search with data analysis:

• "Search for biomarkers of X, then analyze my dataset for those specific markers"
• "Find the standard analysis pipeline for this data type, then apply it to my data"
• "Identify key genes from literature, then check their expression in my samples"

Review and Redirect

Don't just accept every suggestion. After each iteration:

• Check if the findings align with your research goals
• Redirect if BIOS is going down an unproductive path
• Ask for clarification on unclear results
• Request alternative interpretations

Worst case: take stock of your progress and start over - science is iterative, after all!

Data Usage

If you have data to analyze, upload it at the start of your session and describe what it is in your question. Don't just upload—explain the data type, what the columns represent, and what you want to learn from it. This allows BIOS to:

• Reference your data when planning tasks
• Combine literature findings with your specific dataset
• Suggest relevant analyses based on your data type

You can upload data or paste a URL if the dataset is publicly available—no need to download and re-upload. To increase the chances of success, provide the direct download URL rather than a general overview page.

For example:

Maximum upload size is 2GB per iteration.