BONSAI - 2018 - Annual activity report

BONSAI

Project-Team Bonsai

Overall Objectives

Research Program

New Software and Platforms

New Results

Partnerships and Cooperations

Dissemination

Bibliography

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Section: Dissemination

Teaching in computer science:

License: J.-S. Varré, Programming and algorithms, 36h, L2 Computer Science, Univ. Lille.
License: J.-S. Varré, Object oriented programming, 36h, L2 Computer Science, Univ. Lille.
License: J.-S. Varré, Algorithms and data structures, 50h, L2 Computer science, Univ. Lille.
License: J.-S. Varré, System, 84h, L3 Computer science, Univ. Lille.
License: P. Marijon Databases, 36h, L3 Computer science, Univ. Lille.
License: Q. Bonenfant Databases, 36h, L3 Computer science, Univ. Lille.
Licence: M. Pupin, Programming (Python), 78h, L1 Sciences, Univ. Lille.
Licence: M. Pupin, occupational integration, 30h, L3 computer science, Univ. Lille.
Master: : M. Pupin, Programming (JAVA), 24h, M1 “Mathématiques et finance”, Univ. Lille.
License: M. Salson, Programming (Python), 42h, L1 Sciences, Univ. Lille.
License: M. Salson, Coding and information theory, 63h, L2 Computer science, Univ. Lille.
Master: M. Salson, Software project, 40h, M1 Computer science, Univ. Lille.

Teaching in bioinformatics:

Master: M. Pupin, M. Salson Bioinformatics, 34h, M1 ”Biologie-Santé“, Univ. Lille.
Master: M. Salson, Algorithms for life sciences, 20h, M2 Complex models, algorithms and data, Univ. Lille.
Master: R. Chikhi, Bioinformatics, 20h, M1 Computer Science, Univ. Lille.

Teaching in skeptical thinking:

Master: M. Salson, Skeptical thinking, 27h, M2 Journalist and Scientist, ESJ, Univ. Lille.

Formation for academics:

Bilille permanent training: C. Saad (Variants, 13h), R. Chikhi (De novo assembly and Metagenomics de novo assembly, 8h), H. Touzet (DNA analyis and Metagenomics, 8h), M. Salson (RNA-seq analysis, 1h).
(JC)2BIM summer school: H. Touzet organized a national summer school in bioinformatics (5-8 June, Frejus), that gathered 30 participants and 12 trainers (among them, R. Chikhi and M. Salson): http://www.gdr-bim.cnrs.fr/?page_id=560.
Workshop on Genomics: R. Chikhi (de novo assembly & k-mers, 8h), Czech Republic, 2 weeks, 80 participants: http://evomics.org/workshops/workshop-on-genomics/2018-workshop-on-genomics-cesky-krumlov/.
CGSI summer school: R. Chikhi (de novo assembly, metagenomics, two keynote lectures), Los Angeles, 4 weeks, 100 participants: http://computationalgenomics.bioinformatics.ucla.edu.

Head of the licence semester “Computer Science – S3 Harmonisation (S3H)”, Univ. Lille (L. Noé).
Member of faculty council (M. Pupin, J.-S. Varré).
Head of the 3rd year of licence of computer science, Univ. Lille (J.-S. Varré).
Head of the GIS department (Software Engineering and Statistics) of Polytech'Lille (S. Janot).
Head of the computer science modules in the 1st year of Licence, Univ. Lille (M. Pupin).
Head of the Informatique au féminin, Univ. Lille (M. Pupin).

PhD: T. Rocher, Indexing VDJ recombinations in lymphocytes for leukemia follow-up, February 2018, M. Giraud, M. Salson.
PhD: C. Saad, Caractérisation des erreurs de séquençage non aléatoires, application aux mosaïques et tumeurs hétérogènes, September 2018, M.-P. Buisine, H. Touzet, J. Leclerc, L. Noé, M. Figeac.
PhD in progress: P. Marijon, Analyse de graphes d'assemblage issus du séquençage ADN troisième génération, 2016, R. Chikhi, J-S. Varré.
PhD in progress: Q. Bonenfant, Algorithmes pour l'analyse de séquençage ARN troisième génération, 2017/11/15, L. Noé, H. Touzet.

H. Touzet was member of the PhD juries of Camille Marchet (University of Rennes 1), Magali Dancette (University of Lyon 1), Aurélien Quillet (University of Rouen).
H. Touzet was member of hiring committees (professors) at University of Lille and University of Caen.
J.-S. Varré was member of a hiring committee (professors) at University of Lille.
L. Noé was member of a hiring committee (associate professor) at University of Lille.
R. Chikhi was member of the PhD juries of Florian Plaza Onate (INRA MetaGenoPolis), Sorina Maciuca (Wellcome Trust, UK).
R. Chikhi was member of a hiring committee (research engineer) at Institut Pasteur, Paris.

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