Topic outline

  • Links to this Training website

  • Training overview

    Highlighted

    Training overview
    PHENET and EMPHASIS-GO communities share converging data management issues and needs. To this end, we are organising a data management training course in Paris on 04, 05 and 06 December, open to the PHENET-EMPHASIS community.

    Pedagogical objectives
    At the end of this course, participants will have acquired theoretical and practical knowledge of :
    * the management of plant phenotyping data in accordance with FAIR principles
    * the use of plant community (meta)data standards.
    They will also have standardised a dataset in MIAPPE format and identified ways of improving the management of their data.
    This training is organised by PHENET and EMPHASIS with support from URGI.
     Enquête de satisfaction d'une formation organisée par l'URGI

  • Practical Information

    Paris - 04, 05 & 06 December

    Venue: the training will take place at the Hôtel Mercure Paris Centre Gare Montparnasse
    You're invited to join us for lunch at 12:00 on 4th of December. The training will start at 1pm and finish on Friday at 4.30pm.
    This training is funded by Phenome-Emphasis.fr and EMPHASIS-go.

    Templates links:
    The training datasets are available at the bottom f this page

  • Trainers

    Cyril Pommier (INRAE)
    Isabelle Alic (INRAE)
    Farzaneh Kazemi Pour (INRAE)
    Peter Selby (Cornell)
    Sebastian Beier (FZ Juelich)
    Sylvain Poque (University of Helsinki)
    Salvatore Cuomo (University Napoli)
    Sven Warris (WUR)
    Yin Chen (EGI)

    Organisers
    Carla Pinheiro
    Silvana Moscatelli
    Christina Gacic

  • AGENDA

    Wednesday 4/12Thursday 5/12Friday 6/12
    First hands On, bring your own data : File template
    Sequence data management
    Bring Your Own Data!!
    Hands on submission @ EBI
    Sebastian Beier (FZ Juelich)
    Variable building in the MIAPPE template
    Isabelle Alic, Farzaneh Kazemipour,
    Cyril Pommier (INRAe)
    Break
    PHIS: introduction to the Phenotyping Hybrid Information System - Isabelle Alic
    15 ' Break & Menti
    Cloud infrastructure: deploy your own analysis workflow
    Yin Chen (EGI)
    Welcome & Lunch
    Lunch
    Lunch
    Introduction & organisation
    Hands On, Bring Your Own Data (PHIS, File, ...)
    Isabelle Alic, Farzaneh Kazemipour
    FAIR data and metadata
    Farzaneh Kazemipour, Cyril Pommier (INRAe)
    Helsinki Feedback: data traceability, image and data management
    Sylvain Poque (University of Helsinki)
    Data standards for biologists
    (MIAPPE & Crop Ontology)
    Cyril Pommier
    Submission in Dataverse & Zenodo (Canceled to save time for the other hands on)
    Cyril Pommier
    WUR ISA Based File solution (presentation + hands on)
    Sven Warris (WU, NPEC)
    BreakBreak
    Workflows (AGENT) & DMP pragmatic
    and usefull usage for RDM
    Cyril Pommier
    Images information extraction and management using AI
    Salvatore Cuomo (University of Naples)
    Wrap up, questions, last hands on, Menti closing
    Data standards for computer scientists
    Peter Selby (Cornell University)
    Feedback / discussion introduction / Menti
    Carla Pinheiro (NOVA-FCT)
    Dinner on your ownSocial Diner

  • Overview of Plant Data Management principles

    FAIR data and metadata
    Farzaneh Kazemipour, Cyril Pommier (INRAe)
    Data standards for biologists (MIAPPE & Crop Ontology)
    Cyril Pommier
    Break
    Workflows (AGENT) & DMP pragmatic and usefull usage for RDM
    Cyril Pommier
    Data standards for computer scientists
    Peter Selby (Cornell University)
  • Hands On : file template and PHIS database

    First hands On, bring your own data : File template
    Variable building in the MIAPPE template
    Isabelle Alic, Farzaneh Kazemipour,
    Cyril Pommier (INRAe)
    Break
    PHIS: introduction to the Phenotyping Hybrid Information System - Isabelle Alic
    Lunch
    Hands On, Bring Your Own Data (PHIS, File, ...)
    Isabelle Alic, Farzaneh Kazemipour
    Submission in Dataverse & Zenodo
    Cyril Pommier

    Dataverse & Zenodo submission

    To replace this section, attendees can access a previous recording on this subject as well as the presentation material.

  • Images information extraction and management using AI

  • Sequence data management & Cloud infrastructure

    Sequence data management
    Bring Your Own Data!!
    Hands on submission @ EBI
    Sebastian Beier (FZ Juelich)
    15 ' Break & Menti
    Cloud infrastructure: deploy your own analysis workflow
    Yin Chen (EGI)

  • User feedback

    Helsinki Feedback: data traceability, image and data management
    Sylvain Poque (University of Helsinki)
    WUR ISA Based File solution (presentation + hands on)
    Sven Warris (WU, NPEC)

    Helsinki Feedback: data traceability, image and data management,

    See the following jupyter notebook PHIS-Data Import: 2024_PHIS-Data Import_Paris-PHENET.ipynb - Colab

  • Attendees and trainers Photos

    Thanks everybody!