Applied Mathematics and Computer Science Unit from the Genome to the Environment (MaIAGE – UR INRAE)

What Applied Mathematics and Computer Science Unit from the Genome to the Environment (MaIAGE – UR INRAE) does

MaIAGE (UR 1404) is a French public research unit within INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement), operating at Jouy-en-Josas and affiliated with Université Paris-Saclay. The unit brings together mathematicians, computer scientists, bioinformaticians, and biologists to develop methods applied to biology and agro-ecology across scales from molecular to landscape. It is structured into five teams: Dynenvie (dynamic and statistical modeling for ecosystems, epidemiology, and agronomy), Bibliome (knowledge extraction from scientific text), BioSys (systems biology), StatInfOmics (bioinformatics and statistics of omics data), and Migale (bioinformatics platform). Leadership consists of Unit Director Béatrice Laroche and two Deputy Directors, Gwenaëlle André and Sandra Dérozier, with each team led by a designated responsible (Estelle Kuhn, Robert Bossy, Laurent Tournier, Mahendra Mariadassou, Valentin Loux).

MaIAGE develops original mathematical and computational methods with strong competencies in statistical inference, dynamic modeling, automatic control, optimization, algorithmics, and NLP/ML. The unit maintains a substantial open-source software portfolio including AlvisNLP (configurable corpus processing engine), AlvisIR (semantic search framework), AlvisAE (annotation tool with ontology support), RBApy/RBAtools (Resource Balance Analysis modeling for bacteria), BiPSim (stochastic bacterial simulator), CNorm (shallow neural network for entity normalization), re-bert (BERT-based cross-sentence relation extraction), and TyDI (collaborative terminology design). It also produces multi-scale ontologies (BiPON, BiPOm) and reference databases (Omnicrobe) with semantic search, and operates the Migale bioinformatics platform — ISO 9001 certified as part of the BioInfoOmics research infrastructure.

As a French Établissement Public à Caractère Scientifique et Technologique (EPST) entity, MaIAGE does not sell products or services commercially. Activities are funded through government grants, ANR (Agence Nationale de la Recherche) project funding, European Commission grants, and institutional subsidies from INRAE, MathNum, and MICA departments. All software, databases, and publications are distributed freely under open-access or open-source licenses via GitHub, Forgemia INRAE, HAL INRAE, and dedicated web platforms, serving the global life sciences research community rather than paying customers. The unit participates in five INRAE CATI platforms (BOOM, IMOTEP, Modelix, SIP, SOBRE) and is governed by an environmental commitment to a 40% greenhouse gas reduction by 2030 versus 2019 under the GDR Labos 1point5 experiment.

Name

Applied Mathematics and Computer Science Unit from the Genome to the Environment (MaIAGE – UR INRAE)

Legal name

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)

Website

https://maiage.inrae.fr

Company type

Public

Operating status

Operating

Headcount range

1–10 employees

Short description

MaIAGE (UR 1404) is a French public research unit within INRAE that develops mathematical and computational methods for biology and agro-ecology. It operates five research teams and maintains open-source software, ontologies, and databases serving the global life sciences research community.

Ownership category

akta.pro rank

Product category

Computational Biology Research Software

NAICS

Research and Development in the Physical, Engineering, and Life Sciences (54171), Research and Development in Biotechnology (except Nanobiotechnology) (541714), Custom Computer Programming Services (541511)

SIC

Services-Prepackaged Software (7372), Services-Engineering, Accounting, Research, Management (8700)

akta.pro primary industry

Bioinformatics & Multi-omics Analysis Software (HLAGAJAD)

akta.pro secondary industries

Prompt Engineering, Orchestration & LLMOps Tooling (HDAAACAD), AI/ML Engineering & Model Development Services (BPAEAHAF)

Keywords

• Computational biology research
• Bioinformatics software
• Omics data analysis
• Systems biology modeling
• Biomedical text mining

Headquarters

HQ city

Jouy-en-Josas

HQ country

France

HQ region

Europe

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Infrastructure, Operations, Others

Distribution channels4 records

Marketing channels5 records

Core offering

MaIAGE is a public research unit that develops original mathematical and computational methods applied to biology and agro-ecology, spanning molecular to landscape scales. It produces open-source software (AlvisNLP, AlvisIR, AlvisAE, RBApy, RBAtools, BiPSim, CNorm, re-bert, TyDI), reference databases (Omnicrobe), ontologies (BiPON, BiPOm), the ISO 9001-certified Migale bioinformatics platform, and open-access scientific publications and training resources for the life sciences community.

Product overview

MaIAGE (UR 1404) is a research unit developing mathematical and computational methods for biology and agro-ecology. The portfolio includes the Migale bioinformatics platform (ISO 9001 certified), the Alvis Suite (AlvisNLP, AlvisIR, AlvisAE) for text mining and semantic search, RBAtools/RBApy for metabolic modeling, BiPSim for stochastic simulation, TyDI for terminology management, Omnicrobe database, and ontologies (BiPON, BiPOm). These tools support research from molecular to landscape scales, with applications in bioinformatics, NLP, systems biology, epidemiology, and agronomy.

Differentiator

Problem solved

Functional benefit

Brands

• Dynenvie: Dynamic and statistical modeling for ecosystems, epidemiology and agronomy team
• Bibliome
• BioSys
• StatInfOmics
• Migale

Products and services

• Migale Bioinformatics Platform

Quantifiable outcome

• Over 1,300 downloads of the open-access book 'Economic Principles in Cell Biology'
• +2 more outcomes

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

AI capability8 records

Feature10 records

Partnerships

28 partnerships are on record, tiered core, secondary and major.

• INRAE – Institut National de Recherche pour l'Agriculture, l'Alimentation et l'EnvironnementcoreOthersMaIAGE is an INRAE research unit (UR 1404). INRAE is the parent public research institution providing institutional funding, infrastructure, and administrative framework. The unit is administratively and scientifically attached to INRAE, with full institutional support.
• Université Paris-SaclaycoreStrategic or Co-development PartnerMaIAGE is affiliated with Université Paris-Saclay. The unit benefits from academic collaborations, student supervision, and joint research activities through the university. Joint projects and co-supervision of PhD students with university laboratories.
• MathNum Department (Mathématiques et Numérique, INRAE)coreStrategic or Co-development PartnerMaIAGE is attached to the MathNum department of INRAE as the pilot department. MathNum coordinates mathematical and digital research across INRAE and provides strategic direction and funding for the unit.
• MICA Department (Microbiologie et Chaîne Alimentaire, INRAE)secondaryStrategic or Co-development PartnerMaIAGE is also attached to the MICA department of INRAE as a secondary affiliation, contributing to microbiology and food chain research themes.
• BioNLP-ST Shared Task CommunitymajorStrategic or Co-development PartnerMaIAGE's Bibliome team has organized and participated in BioNLP Shared Tasks since 2011 (Bacteria Biotope 2011-2019, SeeDev, Gene Regulation Network, Bacteria Gene Interactions). This ongoing collaboration involves international research teams and drives advancement in biomedical NLP.
• CATI BOOM (Bioinformatics and statistics for Omics and metaOmics of Microbes)secondaryTechnology or IntegrationOne of several CATIs (Automated Centers for Information Processing) that MaIAGE engineers participate in, focused on bioinformatics and statistics for omics and meta-omics of microbes.
• CATI IMOTEP (Information, MOdèles et Traitement des données en Épidémiologie et dynamique des Populations)secondaryTechnology or IntegrationA CATI focused on information, models, and data processing in epidemiology and population dynamics, involving MaIAGE engineers.
• CATI Modelix (Modélisation des connaissances et intégration de données hétérogènes)secondaryTechnology or IntegrationA CATI focused on knowledge modeling and heterogeneous data integration, involving MaIAGE engineers.
• CATI SIP (Service Informatique de Proximité)secondaryTechnology or IntegrationA CATI providing local IT services, involving MaIAGE engineers.
• CATI SOBRE (SOBriété numérique en REcherche)secondaryTechnology or IntegrationA CATI focused on digital sobriety in research, involving MaIAGE engineers.
• Inria BIOCORE TeammajorStrategic or Co-development PartnerCollaborates with Inria BIOCORE team on the InSync project (Intercellular coupling and synchronization between peripheral circadian clocks, ANR 2022-2027) and previously on ICycle project.
• IBV Institut de Biologie de Valrose (Circadian Biology Team)majorStrategic or Co-development PartnerPartner in the InSync project on circadian clock coupling and synchronization, bringing biological expertise on circadian systems.
• CentraleSupélec, Laboratoire MICSmajorStrategic or Co-development PartnerPartner in the ModLSys project (ANR 2023-2028) on multi-scale modeling framework for living systems, providing mathematical and engineering expertise.
• INRAE-AgroParisTech, Institut Jean-Pierre Bourgin (IJPB)majorStrategic or Co-development PartnerPartner in the ModLSys ANR project on multi-scale modeling of living systems, contributing plant biology expertise.
• CNRS-INRAE-UM-InstitutAgro, Institut des Sciences des Plantes de Montpellier (IPSiM)majorStrategic or Co-development PartnerPartner in the ModLSys ANR project on multi-scale modeling framework for living systems.
• INRAE-Micalis (Retro Synthetic Biology Team)majorStrategic or Co-development PartnerPartner in the AMN project (Artificial Metabolic Networks, ANR 2022-2025) on artificial metabolic networks, contributing synthetic biology expertise.
• INRAE-AgroParisTech, MIA Paris-Saclay (EkINocs Team)majorStrategic or Co-development PartnerPartner in the AMN project on artificial metabolic networks, providing mathematical and computational biology expertise.
• CNRS-UGA, Laboratoire TIMCmajorStrategic or Co-development PartnerPartner in the AMN project on artificial metabolic networks, contributing computational modeling expertise.
• CNRS-UCBL, LBBEsecondaryStrategic or Co-development PartnerPartner in the MITOTIC project on metabolic vulnerability in cancer, contributing systems biology and cancer modeling expertise.
• INSERM-UP, Institut CochinsecondaryStrategic or Co-development PartnerPartner in the MITOTIC project on metabolic vulnerability in cancer, contributing biomedical and clinical expertise.
• Institut Micalis (INRAE/AgroParisTech/UPSaclay)majorStrategic or Co-development PartnerCollaborated with Institut Micalis on the study of hypermutators in Bacillus subtilis bacteria, published in Nucleic Acids Research 2025. The unit also contributes to shared supervision of PhD students and joint research projects in microbiology and systems biology.
• LRI (Laboratoire de Recherche en Informatique)majorTechnology or IntegrationCollaborated with LRI on the development of BiPON and BiPOm ontologies, bringing together knowledge representation and semantic web expertise.
• IBV Institut de Biologie de ValrosemajorStrategic or Co-development PartnerPartner in InSync project (ANR 2022-2027) on circadian biology, collaborating with the unit's BioSys team.
• BioinfoRmatique Infrastructure de Recherche BioInfoOmicsmajorStrategic or Co-development PartnerThe Migale platform is a member of the BioInfoOmics Research Infrastructure, collaborating with other platforms on environmental policy and carbon footprint assessment of digital infrastructure.
• GDR Labos 1point5majorStrategic or Co-development PartnerMaIAGE participates in the national GDR Labos 1point5 experiment, adopting a 40% GHG reduction target by 2030 vs 2019, demonstrating environmental responsibility in research activities.
• AgroParisTechmajorStrategic or Co-development PartnerCollaborated on the development of BiPOm ontology and participates in joint research projects. Contributing to the MICA department's food microbiology research.
• GQE (Génétique Quantitative et Évolution)secondaryStrategic or Co-development PartnerCollaborated with GQE on BiPOm ontology development, contributing genetics and evolutionary biology expertise.
• INRAE DSI (Direction des Systèmes d'Information)secondaryTechnology or IntegrationThe unit leverages INRAE's central IT services for additional server capacity needs, using INRAE DSI's rental server offerings rather than expanding its own infrastructure.

Scale indicators6 records

Expansion highlights4 records

Market position

Competitive moat5 records

Key risks6 records

Key highlights7 records

Customer concentration

• LinkedInlinkedin.com/company/unite-mathematique-et-informatique-appliquees-du-genome-%C3%A0-l%E2%80%99environnement-maiage-%E2%80%93-ur-inrae

Compliance1 record

Revenue estimate

Valuation estimate

Number of profiles

Profiles8 records

Funding overview

Funding rounds

Investors

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M&A

Investments

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