Schematic diagrams — visualizing a mechanism

Ask Charlie for a signaling diagram, a project timeline, or a concept map: it will generate a Mermaid diagram right in the chat, complete with references.

Emerit Science Team

Updated: April 2026

Charlie natively generates diagrams in Mermaid format, rendered directly within the conversation. You ask in natural language—Charlie generates the Mermaid code and displays it immediately as an interactive diagram, without the need to copy and paste into an external editor.

And since the diagram is the result of scientific research (PubMed, bioRxiv, HAL…), you’ll find the citations supporting each edge or node right below it.

1. What types of diagrams?

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Flowcharts & Signal Paths

Signaling cascades, regulatory mechanisms, clinical decision trees, experimental workflows.

timeline

Timelines

A timeline of major publications on a topic, the stages of a clinical trial, or the history of a discovery.

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Mind maps

Domain concept map, category hierarchy, structured brainstorming.

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Sequences & Interactions

Sequence diagrams for describing molecular interactions, protocol dialogues, and reaction steps.

2. How to submit the request

No need to learn any specific phrasing. Just ask in French, just as you would a colleague. Here are a few phrases that work well:

→ “Draw me a diagram of the p53/MDM2 pathway, including the main transcriptional targets.”

→ “Create a timeline of major publications on KRAS inhibitors since 2013.”

→ “Create a mind map of the mechanisms of resistance to chemotherapy in triple-negative breast cancer.”

→ “Give me a flowchart showing the activation of the JAK-STAT pathway following IL-6 binding.”

Exemple de prompt et de diagramme Mermaid généré par Charlie

3. Interactive Viewer and Editor

1 The diagram appears directly in the response. Click on it to open the full-screen viewer.
2 In the viewer: zoom, pan, and export to PNG/SVG. Handy for inserting the diagram into a presentation or manuscript.
3 Switch to edit mode to edit a label, add a node, or reposition elements—you'll see the Mermaid code on the left and the preview on the right, in real time.
4 You can also ask Charlie to edit the diagram using natural language: "Add an arrow between p53 and BAX," "Highlight MDM2 in red."

Visionneuse interactive et mode édition du diagramme

4. Supporting citations

Below the diagram, Charlie lists the scientific references used to create it. You can verify the graph’s edges by clicking on the citations—a useful way to ensure that a regulatory mechanism described in the diagram is indeed supported by the literature.

Citations scientifiques sous le diagramme

lightbulb Tip

For signaling pathway diagrams, specify the context ("triple-negative breast cancer," "pancreatic cell"): Charlie narrows the scope and keeps the diagram clear. Without context, you risk ending up with an overly detailed diagram that is difficult to use.

Exemple complet de diagramme avec ses références scientifiques

science What about statistical charts?

Bioinformatics charts (PCA, Volcano, UMAP, QC boxplots) are generated in the Bioinfo module, which is currently available in early access. Request a trial from within the app to join the beta.

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