Information systems

SILEX-LBE -> EnviBIS

SILEX-LBE is the Information System for Experimentation at the LBE Research Unit in Narbonne, which aims to manage data for online monitoring of dry or liquid degradation processes under anaerobic conditions, and microalgae production processes.

Faced with the growing number of biological digestion research processes and the proliferation of sophisticated sensors generating large amounts of measurements, SILEX-LBE enables the collection, centralization, and analysis of this data. It is connected to ODIN (INRIA BIOCORE) acquisition systems, integrating online data from sensors and automated or semi-automated analyzers.

Since it was launched in March 2009, the system has undergone several phases of development. In 2012, it was already managing eight databases covering 40 bioreactors with volumes ranging from 1 L to 25 m³. Today, it acquires and controls data from more than 30 bioprocesses, including five pilot-scale and 26 laboratory-scale processes.

SILEX-LBE is a web-based software program for managing and visualizing bioprocess data. It allows users to compile a complete process history by cross-referencing data from sensors, offline measurements, and maintenance operations, thereby facilitating post-hoc analysis. Its independence from commercial acquisition platforms gives it great flexibility for monitoring innovative processes, while ensuring the traceability of experiments. However, this flexibility requires significant configuration effort for each new deployment.

The development of the system is part of a series of European and regional collaborative projects:

• TELEMAC (2003-2007): founding project dedicated to structuring experimental acquisitions.
• CAFE (2008-2012) and BITA IRSES (2009-2015): extensions to modeling and international scientific exchanges (France-Mexico).
• NoAW (2016-2020): opening and online publication of experimental data using an Open Data approach.
• RIO (2020-2023, Occitanie/Europe regional project): integration of the semantic web into the SILEX ecosystem to improve data structuring and interoperability.

The result of this development is EnviBIS, a new instance based on the OpenSILEX platform, which uses semantic web technologies for bioprocess data management.

This tool is currently being used in several projects:

• BioGazRIO (2020-2023): development of EnviBIS dedicated to bioprocesses, integrating semantic data modeling.
• MeMo (2023-2025): interoperability between EnviBIS and DeepOmics for the joint management of metagenomic and sequencing data.
• MethaSolCN (2025 ongoing): integration of models and near-infrared (NIR) spectrometry spectra for substrate characterization and process analysis.

SILEX-LBE and its EnviBIS variant now constitute a benchmark digital infrastructure for FAIR management of bioprocess data within the LBE, while also serving as a foundation for interoperability and semantic publishing efforts at the European level.

Valorisation :

• Emilie Fernandez, Virginie Rossard, Eric Latrille. Conception d'une ontologie pour la gestion des connaissances en bioraffinerie environnementale, EBO. 8. Atelier INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement (IN-OVIVE), adossé à la conférence Ingénierie des Connaissances @PFIA, IN-OVIVE, adossé à la conférence Ingénierie des Connaissances @PFIA, Jul 2025, Dijon, France. ⟨hal-05073170⟩
• E. Fernandez, A. Bize, E. Desmond-Le Quéméner, V. Rossard, E. Latrille. Combining the analysis of omics data and bioprocess data in environmental biorefineries. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. ⟨hal-04664121⟩
• V. Jamilloux, A. Bize, C. Midoux, A. Gramusset, C. Gil, et al.. DeepOmics, a Digital Environnemental Engineering Platform for Omics data. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. ⟨hal-04619395⟩
• E. Fernandez, A. Bize, E. Desmond-Le Quéméner, V. Rossard, E. Latrille. Creating a comprehensive framework for leveraging meta-omic data in environmental biotechnology processes. Séminaire résidentiel INRAE Semantic Linked Data, CATI DIISCICO; CATI CODEX; réseau In-OVIVE, Oct 2023, Cap d'Agde, France. ⟨hal-04664508⟩
• E. Fernandez, M. Weber, P. Buche, J. Cufi, S. Dervaux, et al.. Alignement et enrichissement d’ontologies utilisées par deux systèmes d’informations gérant des données expérimentales sur les procédés de transformation : OpenSILEX-EnviBIS et PO2 BaGaTel. Atelier IN-OVIVE, organisé dans le cadre de la conférence Ingénierie des connaissances IC-2022, PFIA., Jun 2022, Saint Etienne, France. ⟨hal-03768264⟩
• E. Fernandez, E. Latrille, V. Rossard, D. Garcia-Bernet, A. Battimelli. Livrables Projet BiogazRIO - WP 3.2. INRAE Occitanie Montpellier, 2 place Pierre Viala, 34060 Montpellier. 2022. ⟨hal-04673849⟩
• A. Tireau, P. Neveu, I. Alic, A. Charleroy. OpenSILEX. 2020, ⟨swh:1:dir:ed72e0386747aaf51a0358396832b973a2f446cf;origin=https://hal.archives-ouvertes.fr/hal-04784053;visit=swh:1:snp:6562a4c1d65901e3f719083476f98eb9d1646015;anchor=swh:1:rel:6481341553a6bcdcd9b766a6cb4f08d72f8dd789;path=/⟩. ⟨hal-04784053⟩
• Formation GRP Gestion Répartie de Procédés de 3 à 5 jours selon le public visé en informatique, nous formons des "super-utilisateurs" aux outils de ce système et une formation dédiée aux nouveaux utilisateurs.
• ARTICLE. P. Neveu, V. Rossard, E. Aguera, M. Perez, C. Picou, J.M. Sablayrolles (2008). Gestion de données et de connaissances pour les bioprocédés. EGC  - Atelier Fouille de données temporelles. http://biblio.telecom-paristech.fr/cgi-bin/download.cgi?id=7865
• ARTICLE. Rossard, V., Aguera, E., Neveu, P., Dkhissi, A.-I., Latrille, E., Perez, M., Picou, C., Rozas, N., Sablayrolles, J.-M., Thomopoulos, R. (2010). Utilisation d’ontologies pour la validation de mesures appliquée à la fermentation alcoolique. Cahier des Techniques de l'INRA (69), 51-56.
• Neveu, P., Rossard, V., Tireau, A., Aguera, E., Perez, M., Picou, C., Sablayrolles, J.-M. (2012). Software for data and knowledge management in winemaking fermentations . Presented at KEOD 2012, Barcelone, ESP (2012-10-04 - 2012-10-07).
• Neveu P., Granier A., Koenderink N., Latrille E., Perret B., Rossard V., Tireau A. (2010). CAFE Deliverable 2.2.
• 2014 naissance du système d'information SILEX-MEX, issu de SILEX-LBE.
• A la fin de l’année 2014, SILEX-LBE et ODIN sont repris par une startup BioEnTech qui les fusionne pour donner le logiciel Mémo.

SILEX-LBE languages: PHP, MySQL, HTML, XML, CSS, R, JavaScript, jQuery.
EnviBIS languages: semantic web programming languages (RDF, RDFS, OWL, SParQL), reference ontologies (Dublin Core document, FOAF persons, SOSA sensors, PROV-O provenance), web language (JAVA), database (MongoDB, rdf4j)

Collaboration:  It is based on modular software called OpenSILEX, supported by UMR MISTEA and CATI-CODEX, as well as ODIN software supported by INRIA BIOCORE.

Link with all OTs.

ChemFlow

ChemFlow is an educational information system dedicated to chemometrics, designed to promote the learning and practice of this discipline by as many people as possible, whether they are researchers, students, or laboratory technicians.

The tool is an integral part of the ChemProject, which is structured around three complementary components:

• CheMoocs: a set of free, open online courses dedicated to chemometrics;
• ChemFlow: web-based software for the practical implementation of spectral data processing;
• ChemData: a database for sharing educational examples and spectral resources.

The first session of the CheMoocs MOOC was held from September 16 to November 25, 2016, on the FUN (France Université Numérique) platform. Since then, several editions have been launched, with a gradual division of levels and themes:

• 2017: separation between CheMoocs Basic (October 2–December 3) and CheMoocs Advanced (October 23–December 3).
• 2018–2019: structuring into two independent modules—unsupervised methods (October–November 2018) and supervised methods (February–March 2019).

The initiative arose from an observation: the growing number of spectrometers used in research and industry, which are fast, reliable, and economical tools, is accompanied by an increased need for skills in the chemometric processing of the data generated. However, since the 1970s, France has seen a decline in training in chemometrics, threatening the sustainability of expertise in this field.

The ChemProject was launched with funding from the Agropolis Foundation (2015-2016) and then extended with support from INRAE Occitanie Montpellier's continuing education program. To ensure its continuity, corporate sponsorship was set up via the SupAgro Foundation and the Agropolis Foundation.

Since its creation, the results have been consistent:

• Approximately 1,500 registrants per MOOC session on FUN,
• Nearly 1,000 active ChemFlow accounts,
• More than 45,000 requests processed by the server.

Today, ChemFlow continues to evolve within the ChemProject ecosystem, integrating open science practices, the reuse of spectral data, and statistical processing and online visualization features. Resources and access to the software are available at chemproject.org, which is the gateway to the entire educational platform.

Valorisations :

• plusieurs formations ont été dispensées sur ce logiciel, voir chemproject - Ressources - Formations depuis 2016.
• a fait l'objet de plusieurs présentations
  • M. Naudet-Huart, M. Touratier, J. Regulier, L. Desfontaines, J. Leinster, et al.. Projet INSPIR : Circuit inter-laboratoires du Réseau National INRAE NIRS. Rencontres HélioSPIR 2024, HélioSPIR, Jun 2024, Montpellier, France. pp.11-12. ⟨hal-05182203⟩
  • B. Jaillais, M. Brandolini-Bunlon, J.C. Boulet, G. Chaix, É. Latrille, et al.. ChemHouse, a research and development centre for chemometrics. Congrès Analytics 2022, Sep 2022, Nantes, France. 2022. ⟨hal-03910363⟩
  • C. Chauvergne, L. Bonnal, D. Bastianelli, H. Carrere, Y. Griveau, et al.. Plateforme de modèles locaux/globaux de transfert de spectres inter-instrument. Rencontres HélioSPIR 2019, HélioSPIR, Oct 2019, Montpellier, France. pp.8-9. ⟨hal-05174300⟩
  • V. Rossard, J.C. Boulet, F. Gogé, E. Latrille, J.M. Roger. ChemFlow, chemometrics using Galaxy. Galaxy Community Conference - GCC2016, Indiana University. USA., Jun 2016, Bloomington, United States. ⟨10.7490/f1000research.1112573.1⟩. ⟨hal-01837798⟩poster à HélioSpir 2016
  • D. Bertrand, J. Boccard, M. Boiret, J.C. Boulet, P.  Courcoux, et al.. MOOC CheMOOCS : principes et outils de la chimiométrie pour tous. Doctorat. France. 2016. ⟨hal-02606294⟩
  • et les autres sont consultables sur chemproject.org - Ressources - Publications 
• inscrite au répertoire des plateformes internationales GalaxyProject : https://galaxyproject.org/use/chemflow
• un tutoriel a été rédigé sur chemproject.org - ChemFlow - Tutoriel

Languages: Scilab, Octave (free version of Matlab), R, Julia, Python, postgreSql. It integrates existing chemometric methods into an existing GalaxyProject framework.
Strong collaboration (non-exhaustive) for the development of this software: INRAE-ITAP in Montpellier, INRAE-SPO in Montpellier, France Grille.

Related website: http://chemproject.org

Special link with the MACODE technical office.

TyPol

TyPol, created in 2009 and developed using RStudio, is a micro-pollutant typology information system that classifies organic contaminants not by chemical family, but according to their physicochemical and environmental properties. The criteria taken into account include adsorption, volatilization, transfer to air or water, and toxicological effects.
The processing is based on a multivariate classification performed using data stored in a MySQL database, which allows for flexible and reproducible analysis. This tool, described by Servien et al. (2014), has enabled the classification of more than 300 molecules (pesticides, pharmaceutical compounds, etc.) and is also used to explore the environmental behavior of potential pesticide metabolites (Storck et al., 2016; Benoit et al., 2016).
The issue that led to the creation of TyPol is the very large number of substances to be analyzed, estimated at between 30,000 and 100,000, particularly those subject to regulatory environmental risk assessment (pesticides, substances subject to REACH).

TyPol has two operational objectives:

• To classify molecules into homogeneous groups according to properties such as degradability, mobility, or toxicity.
• To select a model molecule per group in order to focus efforts on more in-depth experimental work or modeling.

Today, TyPol is a reference tool for research on the environmental behavior of organic contaminants, offering both a robust methodological framework and a consolidated database for prioritizing substances of concern and planning targeted experiments.

ARTICLES :

• Rémi Servien, Laure Mamy, Ziang Li, Virginie Rossard, Eric Latrille, et al.. TyPol - a new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior. Chemosphere, 2014, 111, pp.613-622. ⟨10.1016/j.chemosphere.2014.05.020⟩. ⟨hal-00924015v2⟩
• Laure Mamy, Dominique Patureau, Enrique Barriuso, Carole Bedos, Fabienne Bessac, Xavier Louchart, Fabrice Martin-laurent, Cecile Miege & Pierre Benoit (2015) Prediction of the Fate of Organic Compounds in the Environment From Their Molecular Properties: A Review, Critical Reviews in Environmental Science and Technology, 45:12, 1277-1377, DOI: 10.1080/10643389.2014.955627
• Veronika Storck, Luigi Lucini, Laure Mamy, Federico Ferrari, Evangelina Papadopoulou, et al.. Identification and characterization of tebuconazole transformation products in soil by combining suspect screening and molecular typology. Environmental Pollution (1970), 2016, 208, pp.537-545. ⟨10.1016/j.envpol.2015.10.027⟩. ⟨hal-01326180⟩
• Pierre Benoit, Laure Mamy, Rémi Servien, Ziang Li, Eric Latrille, et al.. Categorizing chlordecone potential degradation products to explore their environmental fate. Sciences of the total Environment, 2017, 574, pp.781-795. ⟨10.1016/j.scitotenv.2016.09.094⟩. ⟨hal-01376211⟩
• Harouna Traore, Olivier Crouzet, Laure Mamy, Christine Sireyjol, Virginie Rossard, et al.. Evolution de l’outil de classification in silico TyPol pour analyser et prédire les effets écotoxicologiques des pesticides. 46e congrès du GFP, Groupe Français des Pesticides, May 2016, Bordeaux, France. 1 p. ⟨hal-01608591⟩
• Harouna Traoré, Olivier Crouzet, Laure Mamy, Christine Sireyjol, Virginie Rossard, et al.. Clustering pesticides according to their molecular properties, fate, and effects by considering additional ecotoxicological parameters in the TyPol method. Environmental Science and Pollution Research, 2017, 25 (5), ⟨10.1007/s11356-017-0758-8⟩. ⟨hal-01655395⟩
• Pierre Benoit, Laure Mamy, Dominique Patureau, Eric Latrille, Olivier Crouzet, et al.. Clustering organic contaminants according to their molecular properties, and their environmental fate and ecotoxicological impacts: the TyPol method. EAWAG-INRAE Meeting, Jun 2019, Zurich, France. ⟨hal-03266026⟩
• Kevin Bonnot, Carole Bedos, Laure Mamy, Christian Bockstaller, Eric Latrille, et al.. Estimation du potentiel d’émission des pesticides vers l’atmosphère à partir de leurs propriétés moléculaires avec l’outil TyPol. 49ème congrès du Groupe Français des Pesticides, May 2019, Montpellier, France. ⟨hal-03266404⟩
• Fabienne Bessac, Rémi Servien, Enrique Barriuso, Carole Bedos, Bastien Belzunces, et al.. Chimie théorique et étude du devenir de composés organiques dans l'environnement grâce à l'outil TyPol. International congress "Transitions 2020 - Ecological transitions in transactions and actions" - Colloque international de recherche interdisciplinaire Transitions Ecologiques en transactions et actions, Jun 2020, Toulouse, France. pp.116-118. ⟨hal-03277856⟩
• Laure Mamy, Kevin Bonnot, Pierre Benoit, Christian Bockstaller, Eric Latrille, et al.. Assessment of pesticide volatilization potential based on their molecular properties using the TyPol tool. Journal of Hazardous Materials, 2021, 415, pp.125613. ⟨10.1016/j.jhazmat.2021.125613⟩. ⟨hal-03201288⟩
• Bonnot K., Benoit P., Hoyau S., Mamy L., Patureau D., Servien R., Rapacioli M., Bessac F. 2022. Accuracy of computational chemistry methods to calculate organic contaminant molecular properties. ChemistrySelect, 7, https://doi.org/10.1002/slct.202203586
• Rémi Servien, Coralie Leenknecht, Kevin Bonnot, Virginie Rossard, Eric Latrille, et al.. Improved impact assessment of micropollutants release from WWTPs. Case Studies in Chemical and Environmental Engineering, 2022, 5, pp.100172. ⟨10.1016/j.cscee.2021.100172⟩. ⟨hal-03346134v2⟩

CONFERENCE :

• Pierre Benoit, Laure Mamy, Yoce Aprianto, Dominique Patureau, Eric Latrille, et al.. Future chal- lenges for using in silico molecular typology for risk assessment of pesticides metabolites - the example of Typol. 11th European Modelling Workshop EMW2023 ”Exposure and effect modelling - Linking the domains”, INRAE; Organizing Comittee and Scientific committee: Carola Schriever (BASF), Bernhard Gottesbueren (make-sense consulting), Bas Buddendorf (Wageningen University Research), Thomas Preuss (Bayer AG), Marc Voltz (INRAE), Cécile Dages (INRAE), Sep 2023, Montpellier, France. hal-0433463

POSTER :

• Pierre Benoit, Laure Mamy, Rémi Servien, Eric Latrille, Virginie Rossard, et al.. Categorization of chlordecone potential transformation products to predict their environmental fate. 9. European Conference on Pesticides and Related Organic Micropollutants in the Environment -15. Symposium on Chemistry and Fate of Modern Pesticides, Oct 2016, Saint Jacques de Compostelle, Spain. , 2016. ⟨hal-01604097⟩

It is used as an example in Master's courses (Pierre Benoit, Laure Mamy at AgroParisTech).

Languages: web, R (RStudio, RODBC, RPMG), MySQL. Desire for development: Galaxy, Docker, semantic web.

Strong collaboration (but not exhaustive): internally with LBE OT-Qual-I and more broadly with the EcoSys INRAE joint research unit in Grignon.

Particular link with OT Qual-I and the topic of micropollutants.

ConceptDig

The Concept-Dig project, funded by ADEME (2016-2019) and led by INRAE, aimed to produce a tool to assist in the design of agricultural digestate treatment processes for agronomic use.  This tool is based on a survey of 72 methanization sites belonging to the AAMF (Agriculteurs Méthaniseurs de France) and on experiments and monitoring of digestate treatment processes (phase separation, storage, composting, and incubation on soil).
Based on the digester's input ration, a calculator can predict the agronomic quality of the digestate (biochemical composition and agronomic value as a soil amendment and fertilizer). Based on this data or the results of digestate analyses, other calculators can predict the quality of the treated digestate after phase separation and storage and position it in relation to a typology developed as part of Concept-Dig.

Langages : RShiny (plotly)

Promotion through

• Presentations at national (JRI 2020) and international (Anaerobic Digestion Conference 17, 2022) conferences
• Invention disclosure filed in 2019
• CONCEPT DIG trademark registered (11/23/21), No. 214819581
• APP filing: No. IDDN.FR.001.280008.000. S.P.2022.000.10000 (07/11/2022)
• Web tool launched on the GRDF methanization platform (Oct. 2022)

Projects involved:

• ADEME (2016-2019) led by INRAE
• FertiDig (2021-2024)