What we're building.
Funded projects and open-source tools developed at HolobiomicsLab — from AI agents for mass spectrometry to the MetaboLinkAI Franco–Swiss consortium.
- Active· HolobiomicsLab · 3iA Côte d'Azur · Wimmics (Inria)
Mimosa — evolving multi-agent systems for science
A self-evolving AI framework for autonomous scientific research (ASR) that writes, runs, and improves its own multi-agent workflows — powered by MCP tool discovery and Darwinian evolution.
2026 - Active· ANR (FR) · SNSF (CH) — ANR-24-CE93-0012-01
MetaboLinkAI
A Franco–Swiss consortium developing an AI agent ecosystem for metabolomics — automating data interpretation, annotation, and knowledge integration across mass-spectrometry workflows.
2024 - Active· HolobiomicsLab
Perspicacité — agentic AI literature assistant
An agentic AI assistant for scientists, researchers, and students who want to find and understand academic literature without getting lost in hundreds of papers — local-first, open-source, with multi-agent retrieval and an MCP server.
2025 - Active· HolobiomicsLab · MetaboLinkAI
MetaboT — multi-agent LLM for metabolomics
A multi-agent LLM system that lets researchers explore mass-spectrometry metabolomics knowledge graphs in natural language, translating questions into SPARQL over linked MS data.
2024 - Active· HolobiomicsLab
Toolomics — MCP tooling for scientific agents
An open-source platform for managing and deploying Model Context Protocol (MCP) servers, giving multi-agent systems horizontally scalable access to scientific tools.
2026 - Completed· Académie 1 IdEx UniCA · 3iA Côte d'Azur
KGbot — Knowledge-Graph Chatbot for Metabolomics
An AI system that translates natural-language queries into structured requests over metabolomics knowledge graphs, accelerating hypothesis generation and metabolite annotation.
2024–2025 - Active· EUR Spectrum · 3iA Côte d'Azur
Deep reinforcement learning for MS data acquisition
Offline reinforcement learning that dynamically adjusts mass-spectrometer configurations in real time to maximise the quality and coverage of fragmentation spectra.
2024–2027 - Active· ANR — ANR-24-CE44-1190
ANR POPS — Polyamines in bacterial virulence
Deciphering the role of polyamines in bacterial virulence in Pseudomonas aeruginosa and Staphylococcus aureus, using advanced metabolomics and integrated omics.
2023–2027 - Completed· FNR Luxembourg — project 17994255
Automated MS acquisition for Orbitrap
An automated mass-spectrometry acquisition framework for Orbitrap instruments that enhances the quality and coverage of fragmentation spectra while staying user-friendly.
2024–2026 - Completed· Académie 4 IdEx UniCA
Microbiomics — high-throughput integrative omics
A high-throughput experimental integrative-omics pipeline combining single-cell dispensing with rapid advanced metabolomics and computation to build comprehensive microbial libraries.
2023