Charlie User Guide

The AI Scientific Research Agent. Learn how to use Charlie effectively to accelerate your research, analyze scientific literature and maximize your discoveries.

Emerit Science Team

Updated: May 2026

Interface Charlie - Agent IA de recherche scientifique

Charlie is a scientific research agent powered by a large language model (LLM) and vector search across scientific article abstracts, primarily from PubMed.

It helps you accelerate your research, analyze scientific literature and explore new avenues of inquiry through artificial intelligence. This guide walks you through getting the most out of Charlie step by step.

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What's New in 2026 — Agent Engine v2

Charlie is now based on a multi-agent system (MAS) that provides significant new capabilities.

psychology Reflection Mode — an orchestrator combines multiple searches (scientific databases + the Internet) to produce cross-disciplinary summaries.
memory 4-level memory — Charlie saves data at the session, project, user, and global levels. Your preferences and key facts are preserved from one conversation to the next.
link Unified Citations — a canonical identifier es_id identifies each article, regardless of the source. Automatic deduplication between PubMed, bioRxiv, and HAL.
monitoring New dedicated features: Automated monitoring, Notes, Projects, PDF highlighting.

1. How Does the Search Work?

When a question is asked to Charlie, here is a summary of what happens behind the scenes:

1 It takes into account the conversation history and adjusts its search if needed
2 It compares your question against PubMed article abstracts
3 It selects the 20 most relevant abstracts
4 It generates a response based on the content of these references
5 It displays the references and links to the sources used to answer

2. How to Interact with Charlie?

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

lightbulb The richness comes from dialogue

The more you exchange with Charlie, the more relevant and tailored the responses will be to your context

Steps for a Good Interaction

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Use the year filter
Before asking your question for better temporal focus
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Ask an initial question
Even if it's broad, Charlie will help you refine it
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Let Charlie suggest
Leads and angles of exploration you might not have considered
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Analyze the response
And the sources provided to validate the information
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Dig deeper or pivot
Explore a specific point or discard certain leads

3. Best Practices

To optimize your use of Charlie and get the best results, here are some essential tips:

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Focus on one objective

One objective per session for better consistency in your research and more relevant results

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Use temporal filters

Restrict sources to a more recent period to get up-to-date information

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Organize with colors

Use colors in the interface to categorize your thematic sessions

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Follow your scientific watch

Add relevant references to your library so you can easily refer back to them

4. Example Questions

Here's how to progressively refine your thinking by exchanging with Charlie. These examples illustrate different interaction strategies.

Progressively deepening a subject

→ "What are the known roles of the TGF-β protein in breast cancer?"

→ "And specifically in the regulation of the tumor microenvironment?"

→ "Are there inhibitors targeting this pathway currently in development?"

Redirecting a discussion

→ "I was interested in the role of p53 in apoptosis, but could you instead summarize its involvement in cellular aging?"

→ "Actually, could you compare the functions of p53 with those of FOXO3?"

Specifying a research objective

→ "What strategies are used to deliver siRNA into tumor cells?"

→ "And more specifically 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. Choose the right mode: Snapshot or Reflection

Above the search bar, a settings menu lets you choose how Charlie responds. Two modes, two usage profiles.

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Snapshot

Quick, targeted searches in the scientific database. Ideal for asking a factual question and getting a well-sourced answer in seconds.

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Reflection

Beta

An orchestrator conducts a series of searches (academic databases and the Internet) and synthesizes the different perspectives. This approach is well-suited to cross-cutting or exploratory questions that require a broader perspective.

In the same menu, two model configurations (A and B) are available. Config A prioritizes the quality of reasoning; Config B is sovereign (model hosted in Europe) and suitable for sensitive contexts. You can switch between them as needed—a tooltip displays the characteristics of each configuration.

Two separate toggles complete the setup: "Internet Search" (enables web search) and, from the Library, "Search Library" (searches your PDFs). You can combine them as you like.

6. Getting Started: Signing In, Language, Onboarding

SSO Login

Standard email/password login, or via Microsoft (Entra ID SSO) if your organization has set it up. No need to create a separate password.

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12 languages

The interface is available in French, English, German, Spanish, Italian, Portuguese, Polish, Ukrainian, Dutch, Swedish, Danish, and Norwegian. Change the language from your profile or via ?language=xx the URL.

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Guided onboarding

When you log in for the first time, a step-by-step wizard will walk you through the main features (chat, library, monitoring, feedback). You can access it again later from your profile.

When you configure your filters, you can also choose which databases Charlie searches (PubMed, bioRxiv, HAL, PMC). Disable any that aren’t relevant to your project to reduce noise in the results.

Ready to accelerate your scientific research?

Start using Charlie for free and discover how AI can transform the way you conduct research.

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