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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Logo Principal MUSE Supagro 3BCar Labex IM2E

Laboratory of Environmental Biotechnology

Zone de texte éditable et éditée et rééditée

Information systems

An information system can collect, store, process and communicate information through a set of resources (human, hardware, software, procedures). At the LBE we have developed several SI around the following axes:


SILEX-LBE is the Information System for Experimentation of the UR LBE in Narbonne which aims to ensure the management of data for the online monitoring of degradation processes by dry or liquid means in anaerobic conditions, and process for the production of microalgae.

The problem is the large number of biological digestion research processes at the UR LBE followed by more and more sophisticated sensors which create a large amount of data with their measurement.

It is connected to ODIN (INRIA BIOCORE) acquisition systems for online data from sensors, automated or semi-automated analyzers. In 2012, it managed 8 databases of 40 bioreactors with volumes between 1 L and 25 m3. The SILEX-LBE information system is currently used for the acquisition and control of 5 pilot-scale bioprocesses, and 26 laboratory-scale bioprocesses at LBE. It has been operational since March 2009. In general, Silex is a data management software dedicated to bioprocesses. It makes it possible to collect, display and analyze data collected on bioprocesses, whether it is data measured by sensors, or observations and measurements made by operators. It presents the data via a web interface. It makes it possible to build the history of the process by bringing together sensor data, off-line measurements and maintenance operations, which facilitates the analysis of the data a posteriori. It is independent of a commercial acquisition platform, offers the flexibility needed to monitor innovative processes, and allows the traceability of experiments. The flexibility allows the system to be adapted to each new process. Symmetrically, it requires a significant configuration effort for each new deployment.

It was initiated by a European project Telemac (2003-2007) then it was able to evolve thanks to the European project CAFE (2008-2012) and the Mexican exchange project IRSES BITA (2009-2015). It continues with the European project NoAW (2016-2020) on the "on-line" publication (OpenData) of process data. We will include the semantic web part with the regional Occitanie / European project RIO (2020-2023).



  • GRP training courses in 3 to 5 days, depending on the target audience, we train "super-users" in the tools of this system and training dedicated to new users.
  • ITEM. P. Neveu, V. Rossard, E. Aguera, M. Perez, C. Picou, J.M. Sablayrolles (2008). Data and knowledge management for bioprocesses. EGC - Temporal Data Workshop.
  • ITEM. Rossard, V., Aguera, E., Neveu, P., Dkhissi, A.-I., Latrille, E., Perez, M. Picou, C. Rozas, N. Sablayrolles, J.-M. , Thomopoulos, R. (2010). Use of ontologies for the validation of measurements applied to alcoholic fermentation. Cahier des Techniques of the 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, Barcelona, 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 birth of the SILEX-MEX information system, from SILEX-LBE.
  • At the end of 2014, SILEX-LBE and ODIN are taken over by a BioEnTech startup, which merges them into the Memo software.

Languages: PHP, MySQL, HTML, XML, CSS, R, javascript, Jquery.

Collaboration: It is based on a modular software called SILEX, supported by the UMR MISTEA and the CATI-CODEX, also on the software ODIN carried by INRIA BIOCORE


ChemFlow is an educational IS dedicated to chemometrics.

The objective is to enable a greater number of people to practice chemometrics within the framework of a ChemProject project comprising 3 axes: CheMoocs online courses, ChemFlow software and a ChemData database. The MOOC was opened on the FUN (France Université Numérique) platform for the first session from September 16 to November 25, 2016.

The problem is the very large number of spectrometers sold in research and industry because it is a simple, fast, cheap and reliable tool. Since the 1970s, France has been losing skills in chemometrics due to a lack of training in this field.

It is one of the results of an eponymous project funded first by Agropolis Fondation (2015-2016). This project is continuing thanks to funding from INRA permanent training in Montpellier. The second session of the MOOC was split into 2: CheMoocs Basic (from October 2 to December 3, 2017) and CheMoocs Advanced (from October 23 to December 3, 2017). In 2018, we are at the third session with a new division: unsupervised methods (October-November 2018) and supervised methods (February-March 2019). For the future, we have turned to corporate sponsorship via SupAgro Fondation and Agropolis Fondation.

For 3 years, the results have been the same on average: 1,500 MOOC subscribers via the FUN platform, 600 ChemFlow accounts. The server responded to approximately 45,000 requests. Details for accessing the software are at



  • several trainings have been given on this software, see chemproject - Resources - Trainings:
    • 2016-05-19 in Montpellier as part of the HélioSPIR association (12 participants)
    • 2016-09-12 to 2016-11-25, online course, via the FUN platform (1570 participants)
    • 2016-11-08 in Montpellier as part of the HélioSPIR association (15 participants)
    • 2017-01-30 in Paris at the XVIII chemometrics congress (10 participants)
    • 2017-03-23 ​​and 24 in Avignon as part of the NIRS network (30 participants)
  • has been the subject of several presentations
    • 20 min oral presentation at the GCC 2016 conference in June in Bloomington: Rossard V, Boulet JC, Gogé F et al. ChemFlow, chemometrics using Galaxy. F1000Research 2016, 5:1671 (slide presentation) (doi: 10.7490/f1000research.1112573.1)
    • poster at HelioSpir 2016
    • and the others are available on - Resources - Publications
  • registered in the directory of international platforms GalaxyProject:
  • a tutorial has been written on - ChemFlow - Tutorial

Languages: Scilab, Octave (free from Matlab), R, Python, postgreSql. It integrates existing chemometrics methods into an existing Galaxy framework.

Strong collaboration (not exhaustive) for the development of this software: IRSTEA of Montpellier, INRA-SPO in Montpellier, EIC of Montpellier, INRA-GenoToul, France Grille.

Related website: Special link with OT SAMI.



TyPol is a typology of micropollutants to classify organic contaminants according to environmental properties and molecular characteristics.

The objective is to study the behavior of organic contaminants.

The problem is the very large number of molecules to be analyzed between 30 000 and 100 000 substances concerned by the environmental risk assessment (Pesticides, REACH).

We therefore created this tool to:

  • classify molecules into groups according to different properties (degradation, mobility, toxicology, ...)
  • and choose one molecule per group for further experiments

 This tool was able to evolve in the framework of different projects:

  • 2009-2011: innovative project of the department EA
  • 2011 - 2013: BIODECHLORD - AIP DEMICHLORD 2010: search for the biological signature of the degradation of chlordecone in the soils of the West Indies
  • 2012 - 2014: IMPEC - APR Pesticide MEDDE 2011: development of microbial indicators for assessing the impact of pesticides on terrestrial and aquatic ecosystem functions
  • 2016-2018: Digestate - ANR 2015: diagnosis of Waste Treatments for Contaminants Fates in the Environment
  • 2019-2020 : RhizoPharma - Scientific challenge of the EA Department - "Evaluation of the soil-plant transfer of pharmaceutical compounds brought to the soil by MAFORs using the RHIZOtest". Coordinated by Claire-Sophie Haudin (AgroParisTech).
  • 2019-2020 : PhyLoDispo - Scientific challenge of the EA Department - "Development of Physicochemical tools to characterize the location of pesticides in volcanic soils and assess their environmental availability". Coordinated by Antoine Richard (INRAE).
  • 2017-2020 : RePP’Air - Reduction of Phytosanitary Products in the Air?
  • 2019-2021 : OFB, French biodiversity office (ex AFB, ex ex ONEMA)
  • 2021-2024 : TAPIOCA "Characterize chronic exposure to transformation products of plant protection products and their ecotoxic effects in aquatic environments" (Ecophyto II + Plan - Procedure Call for innovation research or action research projects 2019 "Plant protection products: from exposure to impacts on human health and ecosystems ”) coordinated by Christelle Margoum from INRAE (Lyon)

This tool has been the subject of various valuations:

  • highlight of the EA department in 2013,
  • it was chosen as a milestone for the center of Versailles in 2014.
  • the article "TyPol-Reppair" published in JHM is elected highlight in 2022:
    • Chemosphere in 2014. R. Servien, L. Mamy, Z. Li, V. Rossard, E. Latrille, F. Bessac, D. Patureau, P. Benoit. TyPol-A new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior, Chemosphere, 111, 613-622)
    • ENVIRONMENTAL POLLUTION 2016 Storck V. Lucini L. Mamy L. Ferrari F. Papadopoulou ES Nikolaki S. Karas PA Servien R. Karpouzas DG Trevisan M. Benoit P. Martin F Identification and characterization of tebuconazole transformation products in soil by combining suspect screening and molecular typology. Environmental Pollution, 208, 537-545
    • STOTEN 2017 - Benoit P., Mamy L., Servien R., Li.Z., Latrille E., Rossard V., Bessac F., Patureau D., Martin-Laurent F. 2017. Categorizing chlordecone potential degradation Their environmental fate. Science of the Total Environment, 574, 781-795
    • Oral communication EGU 2017 - Traoré H, Crouzet O., Mamy L., Sireyjol C., Rossard V., Servien R., Latrille E., Benoit P. Clustering pesticides according to their molecular properties and their impacts by considering additional ecotoxicological Parameters in the TyPol method. Geophysical Research Abstracts, Vol. 19, EGU2017-6863, 2017
    • Journal of Hazardous Materials 2021 - Mamy L., Bonnot K., Benoit P., Bockstaller C., Latrille E., Rossard V., Servien R., Patureau D., Prevost L., Pierlot F., Bedos C. Assessment of pesticide volatilization potentials to atmosphere from their molecular properties using the TyPol tool
  • POSTER. Benoit, P., Mamy, L., Servien, R., Latrille, E., Rossard, V., Bessac, F., Patureau, D., Martin, F. (2016). Categorization of chlordecone potential transformation products to predict their environmental fate. Presented at 9. European Conference on Pesticides and Related Organic Micropollutants in the Environment -15. Symposium on Chemistry and Fate of Modern Pesticides, Santiago de Compostela, ESP (2016-10-04 - 2016-10-07)
  • It is taken as an example in Master courses (Pierre Benoit, Laure Mamy at AgroParisTech).

Languages: web, R (RStudio, RODBC, RPMG), MySQL. Desire of evolution: Galaxy, docker, web semantics.

Strong collaboration (but not exhaustive): internally LBE OT-MaXIP and more widely with the EcoSys INRA Grignon UMR.

OT Qual-I and micropolluants theme.


The Concept-Dig project funded by ADEME (2016-2019) and led by INRAe aimed to produce a tool to help design an agricultural digestate treatment chain for their agronomic use. This tool is based on a survey of 72 AAMF (Agriculteurs Méthaniseurs de France) methanisation sites and on experiments and monitoring of digestate treatment processes (phase separation, storage, composting and incubation on soil). From the input ration of the digester, a calculator makes it possible to predict the agronomic quality of the digestate (biochemical composition and amending and fertilizing agronomic value). From these data or digestate analysis results, other calculators make it possible to predict the quality of the digestate treated after phase separation and storage and to position the latter in relation to a typology carried out within the framework of Concept -Dig.


Languages : RShiny (plotly)

Online :

And soon on :

OT Qual-I and digestats theme.