EuroMarine Open Science Exploration (EMOSE) 2017 EditionInternal

Inter-comparison of Marine Plankton Metagenomic Methods

EMOSE

Activity Overview

Type: Capacity building and training
, Type: Course
Start Date: September 11, 2017
End Date: September 15, 2017
Host: CIIMAR
Venue: Porto, Portugal
Contact: Stéphane Pesant
E-mail: spesant [at] marum.de
Funding Call: EuroMarine 2016 Call for Proposals
Total Budget: €27,120
Funds Granted: €10,000

Manager(s): Stéphane Pesant
Co-organiser(s): Tim Deprez, Ivo Grigorov, Catarina Magalhães, Alessandro Vezzi, Francesca Malfatti
Application/registration deadline: May 5, 2017
Registration website: https://goo.gl/forms/GPx8jrjg08TmjfSl1

The 2017 edition of EMOSE will be held in Porto at the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR, University of Porto).

HOW TO APPLY: apply online before 5 May 2017

OUTCOME: all applicants will be informed by email on 31 May 2017

COURSE FEE: 200€

ACCOMMODATION & MEALS: EuroMarine sponsors the costs for all participants.

TRAVEL: EuroMarine sponsors a maximum of 400€ per participant.

MORE DETAILS: online

ORGANISERS: Stephane Pesant (MARUM), Tim Deprez (UGent), Ivo Grigorov (DTU Aqua), Catarina Magalhaes (CIIMAR), Alessandro Vezzi (UniPd) and Francesca Malfatti (OGS).

CONTACT: Stéphane PESANT (spesantatmarum [dot] de)

Topic

This proposal contains elements of three EuroMarine activity categories: It is foremost a novel and innovative way to build capacity and to train early career scientists (CBT-NC); It also has elements of a foresight workshop (FSW) because it reviews current trends (here next generation sequencing) and leads to a review paper. Finally it has elements of a service workshop (SW) because it evaluates open access resources that could be adopted by EuroMarine as a generic service to its community. 

The 12 early-career-scientist participants will be selected based on their experience with marine microbiome analysis and current research activities. They should be postdocs or recently appointed researchers from as many different institutions/countries as possible. Gender balance will also be considered. For the first edition, participation is restricted to EM full and invited members in order to stress the benefits of being part of the EM network. Special care will be taken to include participants with experience with protocols from Tara Oceans, Malaspina, Ocean Sampling Day and Earth Microbiome. EMOSE will be led by Stephane Pesant (MARUM), Tim Deprez (UGent), Ivo Grigorov (DTU Aqua), Catarina Magalhaes (CIIMAR), Alessandro Vezzi (UniPd) and Francesca Malfatti (OGS).

Objectives:

  1. Train 12 early career scientists in using Open Science resources;
  2. Train 12 early career scientists in Marine Microbiome Analysis Methods;
  3. Publish a methodological paper in open access;

Expected Outcomes:

  1. Test existing open science resources and provide feedback to open source and commercial developers;
  2. Deliver a proof of concept and a proposal for the development of an EuroMarine Open Science Service (EMOSS) in support to future EM Workshops and Working Groups; and
  3. Communicate the proof of concept to the EC Open Science Policy Platform.

The 2017 edition of EMOSE will be held in Porto at the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR, University of Porto).

EMOSE will be led by Stephane Pesant (MARUM), Tim Deprez (UGent), Ivo Grigorov (DTU Aqua), Catarina Magalhaes (CIIMAR), Alessandro Vezzi (UniPd) and Francesca Malfatti (OGS).

HOW TO APPLY: apply online before 5 May 2017

OUTCOME: all applicants will be informed by email on 31 May 2017

COURSE FEE: 200€

ACCOMMODATION & MEALS: EuroMarine sponsors the costs for all participants.

TRAVEL: EuroMarine sponsors a maximum of 400€ per participant.

MORE DETAILS: online

ORGANISERS: Stephane Pesant (MARUM), Tim Deprez (UGent), Ivo Grigorov (DTU Aqua), Catarina Magalhaes (CIIMAR), Alessandro Vezzi (UniPd) and Francesca Malfatti (OGS).

CONTACT: Stéphane PESANT (spesantatmarum [dot] de)

The scientific objective of the first Edition (2017) of EMOSE is to review methods in marine plankton metagenomic analysis, essentially comparing the different filtration, sequencing and analysis pipelines used by recent initiatives, i.e. Tara Oceans, Malaspina and the Ocean Sampling Day. An intensive field/lab work was carried out in April 2017 to compare protocols used in the three initiatives. Samples were sequenced during summer at the Genoscope, deposited in open access at INSDC/ENA in August and processed by the metagenomics pipeline of EBI in time for the Hackathon held in Porto 11-15 September. The Hackathon gathered the six organisers, three invited experts from USC (Fuhrman), EBI (Mitchell) and Genoscope (Poulin), and 18 early career bioinformaticians. Twelve of the 18 participants are from EuroMarine member institutions. The bulk of the analyses were done during the 5‐day hands‐on session in Porto, and an ongoing virtual research environment will be used to plan the analysis and to work‐up a review paper.

Field/Lab work pictures: https://drive.google.com/file/d/0ByQ7S8NsOMbpVHI5RGlRVlpjMW8/view?usp=sharing

Hackathon programme: https://docs.google.com/presentation/d/1UAtKWQr-bTzkWtUGzwUFFrlSjJ3oNiU3PiX1XyKtnmE/edit?usp=sharing

Hackathon presentations: https://drive.google.com/drive/folders/0ByQ7S8NsOMbpV1oxVUZ4cVRBS2M?usp=sharing

Group Picture: https://drive.google.com/file/d/0ByMpTdkzpJHXUUh2QVFrSWh4V1k/view?usp=sharing