Best Practices for Using Charlie

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

Emerit Science Team

Updated: May 2026

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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Avoiding outdated information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 Library

When you use the Library 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 Library. This allows you to track your scientific research and build a personalized collection.

Add a PDF to your library from the results on Charlie

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?

8. Master the tools for everyday conversation

Charlie highlights several small, unassuming yet useful tools that can make your workflow much smoother. Here’s an overview.

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Voice dictation

Click the microphone icon in the search bar to speak your question. This is handy when you're on the go or want to ask a long question without using the keyboard.

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Ending a generation

While a response is being generated, a "Stop" button replaces the "Send" button. You can stop the generation process and immediately rephrase it—no need to wait until it's finished if you see that it's not going in the right direction.

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Export a response as a PDF

For any response from Charlie, the "Export to PDF" feature generates a clean document that includes tables, formatting, and clickable citations. This is useful for sharing a summary outside the platform.

Share an article

On the page for a cited article, the Share button generates a permalink (/article/...) that you can send to a colleague. It takes them to the same article page, with access to the PDF if available.

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Provide feedback to the team

The feedback button (the message bubble in the bottom right corner of the app) opens a form where you can share your immediate thoughts—bugs, suggestions, or comments on a response. Your feedback directly drives improvements to Charlie.

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!

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