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Laboratory of Environmental Biotechnology

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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

SILEX-LBE is the Information System for the LBE UR Experiment in Narbonne, the aim of which is to ensure the data management for on-line monitoring of dry or liquid degradation processes under anaerobic conditions, and method of producing microalgae. The problem is the large number of processes of research of biological digestion at UR LBE followed by more and more sophisticated sensors which create a large number of data with their measurement. Inline data from sensors, automated or semi-automated analyzers is connected to ODIN acquisition systems (from INRIA BIOCORE). In 2012, it manages 8 databases of 40 bioreactors with a volume between 1 L and 25 m3. The SILEX-LBE information system is now used for the acquisition and control of 5 bioprocesses of pilot size and 26 bioprocesses of laboratory size at the LBE. It is operational since March 2009. In general, Silex is a data management software dedicated to bioprocesses. It collects, displays and analyzes data collected on bioprocesses, whether it is data measured by sensors, or observations and measurements carried out by operators. It presents the data via a web interface. It makes it possible to construct the process history by combining sensor data, off-line measurements and maintenance operations, which makes it easier to analyze the data a posteriori. It is independent of a commercial acquisition platform, offers the flexibility to monitor innovative processes, and allows the traceability of the experiments. Flexibility makes it possible to adapt the system to each new process. Symmetrically, it requires a major configuration effort for each new deployment.

It was initiated by a European project Telemac (2003-2007) and then evolved thanks to the European project CAFE (2008-2012) and the IRSES project of Mexican exchange BITA (2009-2015). It continues with the European project NoAW on OpenData ("OpenData)" on-line process data.

Valuation:

  • 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. http://biblio.telecom-paristech.fr/cgi-bin/download.cgi?id=7865
  • 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

ChemFlow is a pedagogical IS dedicated to chemometry.

The aim is to allow a greater number of chemometric studies to be carried out within the framework of a ChemProject project comprising 3 axes: CheMoocs online courses, ChemFlow software and ChemData database. The MOOC was opened on the FUN (France Université Numérique) platform for the first session from 16 September to 25 November 2016.

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

This is one of the results of an eponymous project funded first by Agropolis Foundation (2015-2016). This project continues in a second session of the MOOC, which was split into 2: CheMoocs Basic (2 October to 3 December 2017) and CheMoocs Advanced (23 October to 3 December 2017) via the FUN platform. This re-broadcast was financed by the INRA permanent formation in Montpellier. For the future we have turned to corporate sponsorship via SupAgro Foundation and Agropolis Foundation.

Result: 1570 enrolled in MOOC via the FUN platform, 630 ChemFlow accounts. The server responded to 47000 queries. This software is accessible from the address opposite: https://vm-chemflow.toulouse.inra.fr

Valuation:

• several training sessions were given on this software

  • 2016-05-19 in Montpellier within the framework 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 within the framework of the HélioSPIR association (15 participants)
  • 2017-01-30 in Paris at the congress of chemometry XVIII (10 participants)
  • 2017-03-23 and 24 in Avignon as part of the NIRS network (30 participants)

• a 20-minute oral presentation at the GCC 2016 conference in Bloomington in June: Rossard V, Boulet JC, Gogé F et al. ChemFlow, chemometrics using Galaxy. F1000Research 2016, 5: 1671 (slide presentation) (doi: 10.7490 / f1000research.1112573.1)

• A tutorial was written: http://chemproject.org/wakka.php?wiki=AideChemflow

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

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

Associated website: http://chemproject.org

TyPol

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

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.
  • ARTICLE.
    • 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
  • TO POST. 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) http://prodinra.inra.fr/record/395730
  • 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.

Contact

Eric Latrille