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Chairs and leads


Scientifics events organised by the unit and leads animated by the unit

Réseau(x) ou collectif(s) de recherche


D2K :
De la Donnée à la Connaissance (2015-2017)
Web site : https://digicosme.lri.fr/tiki-index.php?page=GT%20D2K

Groupe de travail du Labex DigiCosme

Réunion bimensuelle

Sur le thème de la "Résolution de questions complexes suivant un point de vue guidé par la tâche, combinaison de méthodes interdisciplinaires allant du traitement des données et de l’information à celui de la connaissance". Exemples de sujets traités :  "Modélisation et Processus", "Connaissances et Analyse d'images", "Connaissances et Raisonnement", "Analyse de contenus multimedia", "Compétitions en text-mining dans le domaine biomédical"

Contacts : Chantal Reynaud (LRI), Claire Nédellec (MaIAGE)


Réunions bioinformatiques de Jouy-en-Josas :
Réunions des bioinformaticiens du centre de Jouy-en-Josas (depuis 2012) Jouy-en-Josas
Member(s) of the relevant unity for the animation : Sandra Dérozier, Cyprien Guérin

Ces réunions permettent un regroupement des bioinformaticiens du centre de Jouy-en-Josas afin de discuter autour des thématiques de chacun. Ces réunions permettent de partager autour de ses activités, de faire de la veille technologique et scientifique. Des réunions ouvertes sur le centre à destination de l'ensemble du personnel ont organisées chaque année.


Stratège :
Statistique en Écologie et données Génomique (depuis 2017) Paris
Member(s) of the relevant unity for the animation : Mahendra Mariadassou, Sophie Schbath

Web site : http://maiage.jouy.inra.fr/?q=fr/stratege

Le réseau a pour objectif de réunir des statisticiens (intéressés par l'écologie appliquée) et des écologues (intéressés par la modélisation statistique) qui fondent leurs recherches sur des données génomiques. Il cherche à favoriser les interactions entre ces deux communautés, à créer une culture scientifique commune et à partager les méthodes et cadres méthodologiques.

Evènement(s) scientifique(s)


GCC2017 :
Galaxy Community Conference (26-30 juin 2017) Montpellier
Member(s) of the relevant unity for the animation : Olivier Inizan

Web site : https://gcc2017.sciencesconf.org/

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, demos, poster sessions, lightning talks and birds-of-a-feather gatherings, all about high-throughput biology and the tools that support it.  GCC2017 will include keynote talks and exhibitors, and plenty of networking opportunities. There are also three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.


RCAM'17 :
Recent Computational Advances in Metagenomics (9-10 octobre 2017) Paris
Member(s) of the relevant unity for the animation : Valentin Loux, Mahendra Mariadassou, Sophie Schbath

Web site : http://maiage.jouy.inra.fr/?q=fr/rcam2017

This workshop aims at promoting discussions and collaborations between biologists (modelers), computer scientists and applied-mathematicians involved in metagenomics and/or metatranscriptomics studies, either in the bioinformatics or statistical aspects of such analysis.


SaMMBA :
Statistical and Mathematical Modeling in Biological Applications (depuis 2011) Institut Pasteur, Paris
Member(s) of the relevant unity for the animation : Elisabeta Vergu

Web site : https://research.pasteur.fr/fr/project/sammba-seminars/

Démarrée en octobre 2011, la série de séminaires mensuels «Statistique et modélisation mathématique pour les applications en biologie » (SaMMBA), propose des conférences et des discussions avec des scientifiques de premiers plan de ces disciplines. L'organisation est assurée par un comité composé de neufs chercheurs modélisateurs d’Ile de France de six laboratoires rattachés à différents organismes (Inserm/UPMC, Institut Pasteur/UVSQ, CNAM, UPS, INRA), visant à regrouper cette communauté. La manifestation a lieu à l’Institut Pasteur à Paris, pour permettre un accès facile de tous les participants.


SMPGD 2017 :
Statistical Methods for Post-Genomic Data. (12-13 janvier 2017) Londres
Member(s) of the relevant unity for the animation : Sylvie Huet

Web site : https://www.smpgd.fr

This workshop aims at gathering statisticians, computer scientists, and biologists to discuss new statistical methodologies for the analysis of high throughput biological data and the challenge arising herein.


StatMathAppli 2017 :
Statistic Mathematic and Applications (4-8 septembre 2017) Fréjus
Member(s) of the relevant unity for the animation : Sylvie huet

Web site : https://colloque.inra.fr/statmathappli

L'objectif du séminaire est d'offrir une opportunité aux jeunes statisticiens de divers pays de se rencontrer et de présenter leurs travaux lors d'un meeting international. Son programme s'articule autour de deux cours dispensés par des chercheurs de renommée mondiale, présentant des méthodes de statistiques mathématiques ou plus généralement de mathématiques appliquées, en relation avec des applications.

En 2017 les conérenciers invités sont Franis Bach pour un cours intitulé "Large-scale machine learning and convex optimization" et Andréa Montanari pour un cours intitulé "Statistics with matrices, graphs, and tensors".


BioNLP-ST :
Workshop BioNLP Shared Task (12-13 August 2016) Berlin, Humbolt University
Member(s) of the relevant unity for the animation : Bibliome team

Web site : http://2016.bionlp-st.org

BioNLP-ST workshop is a joint event with BioASQ. Both are shared task on information extraction from texts in the biomedical domain. The workshop is a joint event with the ACL 2016 conference. This year's theme by INRA: Bacteria Biotopes and Seed Development.


Workshop "Recent Computational Advances in Metagenomics (RCAM)" 2018 :
Workshop "Recent Computational Advances in Metagenomics (RCAM)" 2017 (8 – 12 September, 2018) Athens, Greece
Member(s) of the relevant unity for the animation : Mahendra Mariadassou, Valentin Loux, Sophie Schbath

5th edition of the Workshop 

"Recent Computational Advances in Metagenomics (RCAM'18)"

September 9, 2018

Athens, Greece


OBJECTIVES
---------------
This workshop aims at promoting discussions and collaborations between biologists (modelers),  computer scientists and applied-mathematicians involved in metagenomics and/or metatranscriptomics studies, either in the bioinformatics or statistical aspects of such analysis.
Metagenomics  studies  refer   to  analyses  based  on high-throughput sequencing  of environmental samples  and microbial ecosystems. Both marker-gene (16S, 18S, ITS,  ...)  and whole-genome strategies will be adressed to  cover a wide  array of question ranging  from quantifying the  microbial  diversity in  order  to  find  structuring factors to assessing the functional role of microbial communities.
The workshop will provide  an overview of the state-of-the-art methods currently used in metaomics including comparative metagenomics and metatranscriptomics.  At the  other end  of the  spectrum, case-studies with a strong methodological component will illustrate how and when these methods are useful and how they produce new biological knowledge. This includes studies that investigate the shortcomings of mature or novel methods (e.g. for clustering, inference of co-occurrence networks, detection of certain types of interaction between taxa, etc) in real life settings. 

SCOPE
--------
The program of this workshop will consist mainly of presentations of refereed papers (30 minutes) and  invited talks (50 minutes). A poster session will be also organized. Contributions are welcomed on all aspects  about bioinformatics and statistical analyses of metaomics datasets, including, but not limited to:

  • new methods, tools or pipelines involved in the characterisation of microbial diversity,
  • original methods for taxonomical assignment,
  • Metagenomics/metatranscriptomics assembly,
  • data reduction,
  • comparative metaomics,
  • models for community assembly,
  • inference of co-occurrence/abundance patterns,
  • challenges for tackling the complexity of metaomics datasets.

Note that this workshop focuses mainly on methodological aspects of metagenomics and is not dedicated to bioanalyse result presentations.

KEYNOTES
---------

  • Anton Korobeynikov: "TBA"
  • TBA: "TBA"

PROGRAM [BOOKLET]
---------



SUBMISSION
----------------
Please send the abstract to rcam@jouy.inra.fr

All submitted abstracts will be peer-reviewed by the program committee. Submitted abstracts should not exceed 2 pages including bibliography. Abstracts must be written and presented in English. They may describe work that has already been published or that is simultaneously submitted to a journal, conference, or workshop with reefreed proceedings.

REGISTRATION
----------------
The RCAM worskhop is a satellite workshop of ECCB'18 and registrations fees are those corresponding to ECCB workshops: see here for more information.

IMPORTANT DATES
----------------
Submission Deadline : July 20 at noon
Notification: July 28, 2018
Workshop Date: September 9, 2018. The worskop will start at 9:00am.

ORGANIZERS
------------
Valentin Loux, INRA/MaIAGE, Jouy-en-Josas, France
Mahendra Mariadassou, INRA/MaIAGE, Jouy-en-Josas, France
Pierre Peterlongo, Inria/IRISA, Rennes, France
Sophie Schbath, INRA/MaIAGE, Jouy-en-Josas, France

SPONSOR
------------------
The workshop is supported by the metaprogramme "Microbial Ecosystems and Metaomics (MEM)" from the French National Institute for Agricultural Research (INRA), by the "GdR Molecular Bioinformatics (GdR BiM)" and by the "Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI)" from Institut Pasteur.


Workshop in​ ​ computational​ ​ modeling :
Workshop "Recent​ ​ progress​ ​ in​ ​ computational​ ​ modeling: cells​ ​ and​ ​ cell​ ​ communities" (13-15 novembre 2017) Jouy-en-Josas
Member(s) of the relevant unity for the animation : Anne Goelzer, Wolfram Liebermeister, Vincent fromion

This workshop on modeling cells and cell communities addresses technical challenges
characteristic of complex and modular cell models. The presentations will describe
whole-cell models encompassing metabolism, protein expression, and other cellular
subsystems, as well as multi-cell models describing tissues or microbial communities. In the
practical part of the workshop, we explored automated model construction, submodel
coupling, and possible uses of SBML in setting up heterogeneous cell models. In particular,
we discussed the usage of the SBML “comp” package to couple dynamic and
stoichiometric models, and novel XML and SBML file formats for Resource Balance Analysis
models.



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by Dr. Radut