Best Practices for Using Charlie

Optimize your experience with Charlie by following these recommendations for more effective scientific research.

Emerit Science Team

Updated: January 2026

lightbulb

Key Principle

"The richness comes from dialogue."

Charlie is designed for natural conversation, like a thinking partner. It understands both open-ended and specific questions, and you can structure your research approach step by step.

1. Organize Your Research Sessions

✓ Focus on one objective per session

For better coherence, focus each session on a specific objective. This helps Charlie better contextualize your questions and provide more relevant answers.

Example objectives:

Explore the mechanisms of a specific protein
Analyze a corpus of articles on a specific topic
Develop an experimental protocol
Write a section of a scientific paper

✓ Use colors to organize your sessions

In the interface, use colors to organize your thematic sessions. This helps you easily find your conversations and structure your research work.

Organizing sessions with colors in Charlie

2. Use Filters Effectively

✓ Filter by year for better focus

Use the year filter before asking your question to restrict sources to a more recent period. This is particularly useful for:

Getting the most recent discoveries
Avoiding outdated information
Focusing research on a specific historical period

Using filters (date, article type, language) in Charlie

3. Take a Progressive Approach

Charlie can guide you through a progressive approach. Here's how to structure your research:

1
Ask a first question, even if it's broad
Don't search for the perfect question right away. Start with a general question to explore the topic.
2
Let Charlie suggest avenues to explore
Analyze the response and suggestions to identify interesting angles.
3
Analyze the response and sources
Check the sources in the side panel to deepen your understanding.
4
Dive deeper into one point or set aside another
Progressively refine your research based on the answers you receive.

4. Examples of Progressive Questions

Here are some examples showing how to refine your thinking by exchanging with Charlie:

Progressively deepening a topic

• What are the known roles of the TGF-β protein in breast cancer?
• And specifically in tumor microenvironment regulation?
• Are there inhibitors targeting this pathway currently in development?

Redirecting a discussion

• I was interested in the role of p53 in apoptosis, but can you summarize its involvement in cellular aging instead?
• Actually, can you compare the functions of p53 with those of FOXO3?

Refining a research objective

• What strategies are used to deliver siRNA into tumor cells?
• And particularly in the case of brain tumors?
• Are there approaches using nanoparticles?

Exploring multiple angles

• What are the reported effects of metformin in oncology?
• Are these effects observed independently of diabetes?
• Can you list the mechanistic hypotheses proposed in the literature?

5. Best Practices for the Workspace

When using the Workspace to analyze your own PDF documents:

✓ Prepare your corpus

Import well-targeted documents based on your needs. A coherent corpus will yield better results.

✓ Name your documents clearly

If you want to reference a particular document, give it an explicit name (e.g., "Study_Smith_2023" rather than "article1.pdf").

✓ Analyze from multiple angles

Leverage different perspectives: automatic summary, key points, concepts, methodology, results, etc.

✓ Add relevant articles

Articles automatically found by Charlie can be added to your personal workspace for deeper analysis.

✓ Ask for rephrasing

If the answer is too technical, don't hesitate to ask for a rephrasing in simpler or more detailed terms.

6. Manage Your References Effectively

✓ Add relevant references to your workspace

Use the add feature to save relevant references to your workspace. This lets you track your scientific monitoring and build a personalized library.

Add a PDF to your workspace from Charlie's results

7. What to Avoid

✗ Questions to avoid

✗ "Give me all articles about protein X"

Charlie will provide a selection from the 20 most relevant abstracts available, not an exhaustive list.

✗ "Which articles were written by Dupont?"

Charlie does not yet search by author names ("Deep Search" feature coming soon).

✓ Recommended questions

✓ What are the known mechanisms of protein X in cell signaling?

✓ How is Y involved in the pathogenesis of Z?

✓ What are the reported effects of JAK/STAT pathway inhibition in hematological cancers?

Start Using Charlie Effectively

By following these best practices, you'll get the most out of Charlie to accelerate your scientific research. Remember: the richness comes from dialogue!

Try Charlie for Free