Noel Magnin

• Led digital product development for the ARA companion mobile app at Ecorobotix, a Swiss precision agriculture company. • Analyzed data status, which data is required for project development and completion and identified ways to transform data from the field so that it becomes usable. • Completed Le Wagon bootcamp in Data Science to enhance data analysis and product development skills.

Participation to the development of an epidemiosurveillance app: platform.garden. Development of R&D projects concerning plant pathogens and more generally optimisation of plant growth/well being. Use of remote sensing, biocontrol, and all available solutions to reduce the use of chemicals in the environment. Management of a "Big Data" environment (Azure DataBricks) in collaboration with a computing partner (Agaetis). Daily use of python/SQL to analyse data and extract valuable bio-related results. MS Azure DataBricks / Python notebooks Access to SQL databases : psycopg / sqlalchemy Python : os / pandas / numpy / re (regular expressions) / scipy.interpolate / matplotlib / PIL (image manipulation library) / openpyxl / datetime / json / requests "geoPython" : geopandas / shapely / geojsoncontour / rasterio Javascript

Development of a Biomark-Fluidigm digital PCR system for the evaluation of Biocontrol/biostimulant extracts. Selection of sequences in the grapevine genome, design of primers and test of the primer sets in RT-PCR experiments for their specificity and efficiency. The project aims at finding a way to characterize new extracts in terms of their mode of action in order to use these extracts adequately in the field. The original system which I updated (new sequences versions) targeted sequences specific of secondary metabolism/plant defense and the new one targets genes of the primary metabolism and regulatory functions.

Projects management in the "Pole Biologie et Pathologie" (provides all patient analyses) of the Hospital. The Hospital has set up a large robotic platform (Abbott) for providing health care analyses and a new Laboratory Information Management System (Glims from MIPS society) has been installed. I have provided assistance to the Bioinformatics unit of the hospital in several aspects: • User training: Technicians and Medical Doctors • Users account creation and parameterisation • Medical prescriptions scanning set up • Daily problem solving and users help (remotely accessed computers/on site)

Precision agriculture start-up based on data integration for increased products quality and yields. Main technologies involved : imagery (drone and satellite), soil analyses (physical, mineralogical and biological), meteorology (temperature, humidity), and computing data analytics.

CASDAR (french agricultural agency) contract focused on grapevine trunk diseases. Data curating, analyses, introduction into a web-accessible database according to specifications (plus some improvements). Data related to grapevine trunk diseases: recommendations for better data collection for improvements towards results gained from data analyses, mostly • more precise GPS locations of observations • increasing observation sites Heavy work on data organisation performed for correct exploitation (Perl/Python formatting). Data presentation by generating visualisation graphs in R programming language.

CASDAR (french agricultural agency) project concerning grapevine trunk diseases. Several experiences gained: • RNAseq - biological setup of experiments AND total biocomputing analyses of raw results. • Physiology of a crop-pathogen relationship: laboratory, greenhouses and field approaches, their pros and cons. Precisely: I did set up protocols for high-quality and reproducible mRNA extraction from Vitis wood samples. These mRNA extracts were used for microarray and RNAseq analyses (very high-quality mRNA required). I did set up conditions for high-throughput analyses, performed biocomputing analyses (statistical, biological) and wrote project reports (scientific papers). I managed relations with service providers (I selected the service providers too): • Toulouse Genopole for microarray experiments, • Strasbourg Genopole for RNAseq experiments. I collected resulting data and performed analyses on a personal computer and on remote or local Linux servers. RNAseq data were first analysed (cleaning and statistical part) on the computing cluster of Toulouse Genopole and resulting data analysed on a local server (Biolinux I installed/managed) by several bioinformatics applications. I installed locally a Galaxy environment (http://environmentalomics.org/bio-linux-galaxy/) for all laboratory users and managed this environment for the different useful applications (RNAseq analyses, mothur for high-throughput microbial analyses) and trained the users. Our most important result soon to be published concerns dual RNAseq data from wood-infected grapevine. The protocols I adapted provide molecular data of the fungi during wood infection. More than 30% of the predicted genes from the fungus (Neofusicoccum) were detected in our samples.

Bioinformatic analyses for the Plant Health Unit members (UMR Santé Végétale). Research Project themes: fungi pathogens of grapevine (mildews and esca .....). I was involved in designing high-throughput experiments (microarray, RNAseq) to obtain physiological information about • grapevine responses to pathogens attacks and • pathogens "mode of action". The first project I was involved with concerns the evolution of a low-throughput testing system (qRT-PCR) to a high-throughput system (microfluidic testing) for grapevine pathogen-resistance genes. The original system tested for about 20 genes and I performed the search for genes orthologs (NCBI-Blast) to the 20 original ones and new genes within the grapevine genome. Several genes were found by a thorough bibliographic analysis of most studied plant-pathogen models (Arabidopsis, Nicotiana, ...) and search within a specialised database (Genevestigator). I performed the subsequent search for specific primer pairs for all these genes and participated in the optimisation of the testing protocols.

Bioinformatics for the different research groups involved in research about grapevine physiology : fruit quality / rootstock effects. Informatics (soft and hardware) for the department, setup of the informatics part of a phenotypic platform.

Hospital Bordeaux (Hospital Pellegrin, Bordeaux – Virology Laboratory 02/05 to 08/05) and University Bordeaux 2 (Virology Laboratory - 09/05 to 07/07- French "National Agency for AIDS Research" contract) • Formatting/Integration of biological and clinical data in a relational database, • Management of contacts with Smartgene (service provider) personnel for setting up the database and making adjustments, • VIH / VHC sequences analyses (phylogeny, polymorphism, mutations, and statistics). • Technical assistance for installation of a robotic system (Cobas-Ampliprep-Taqman) dedicated to the extraction of nucleic acids and analysis by qPCR (hospital setting), • Assistance to technical and medical personnel: PCR, sequencing and computing/bio-computing, • Recovery of a sequencing database (Beckman sequencing apparatus - Microsoft Access DB) from an out of order computer and setup of a replacing computer with complete data recovery.

Expert in the evaluation of research projects (Integrated projects), Panel “Food quality and safety” - FP6

I participated in several research projects in relation with biological laboratories, mainly involved in Trypanosoma research and small RNA research. The aim of the projects was to provide analyses of biological data (both in-house produced and collected from biological databases). I performed: • Biological data analysis (DNA and Protein sequences) by EMBOSS software and scripting (Perl, PHP) • Database management (SQL, PostgreSQL) • Programming (Perl, PHP, HTML, SQL, XML) This work allowed the biological laboratories to find new membrane protein as therapeutic targets.

Undergraduate and Post-graduate teaching in biology - plant biology, biochemistry, molecular biology. Bioinformatics and molecular biology contributions to research projects (grapevine secondary metabolism).

Molecular biology and bioinformatics in the program 'TMR network on Green Bacterial Photosynthesis: Structure, Function and Regulation of Light-harvesting Systems and Core Complexes' of the European Community Commission. Research project: Photosynthesis of anaerobic sulfur bacteria : molecular approach. Odense research director : Dr. M. Miller . TMR project coordinator : Prof. Jan Amesz (Netherlands). My work concerned two aspects: • Setup of molecular biology (cloning and sequencing) in the laboratory, • Find point mutations within collected sequences from Chlorobium tepidum, • Generate mutated strains to provide biophysicists with alternative photochemical reaction centers.

USDA-financed project (May 95-May96) : plant physiology, protein biochemistry for the characterisation of a photosynthetic CO2-concentrating system in an aquatic plant (Hydrilla verticillata). I did set up molecular biology approaches (RNA, DNA) and obtained results in the molecular characterisation of the system. Establishment of a program for the pursuit of the molecular work, NSF-financing obtained for the laboratory of Prof Bowes based on the molecular approach.

Research project : Purification and characterisation of the photosystem 2 D1 processing protease in higher plants. PhD thesis supervisor : Prof. J.R. Bowyer - Scientific Counselling : Dr. P.M. Bramley . European commission financing (Science project 1991-1993). Experienced gained at designing protein purification protocols and related technics (enzymatic assay, subcellular fractionation, molecular separation by liquid chromatography, FPLC, HPLC, SDS-PAGE, ...). During the course of the project, the protease was cloned and sequenced by Japanese and American laboratories by gene complementation within a cyanobacteria.