Post on 11-Oct-2020
FAIR ACTIVITIES @ DTL & ELIXIR-NL
Celia van Gelder, Programma Manager DTL Learning/ELIXIR-NL Training Mateusz Kuzak, DTL Scientific Community Manager
April 2018
www.dtls.nl
Non-experimental
data
NL PUBLIC PRIVATE EXPERTISE NETWORK IN DATA INTENSIVE LIFE SCIENCES
WHY DTL? ENABLING CROSS-DISCIPLINARY LS RESEARCH!
Bio-
diversity
Biotech
Agro
Food
Health
Design of experiment
Information & insight
Research Project
Life science objective
Reference data &
Literature
technologies to measure
(meta-)genomics, transcriptomics, proteomics, metabolomics, microscopy,
bioimaging, phenotyping, lifestyle, ….
technologies to deal with databioinformatics, data science, biostatistics,
computational (systems) biology, computer science, e-science, ICT, …
Biomaterial collections
Model systems
www.dtls.nl
>130 EXPERT GROUPS INVOLVED
Nijmegen
Amsterdam
Wageningen
Utrecht
Rotterdam
Eindhoven
Maastricht
Groningen
Leiden
Delft
Enschede
Zeist
Hanze University
University Groningen
UMCG
Hubrecht Institute
UMCU
Utrecht University
Wageningen UR
DLO
TU Twente
Radboudumc
Radboud University
Maastricht University
MUMC+
CTMM
TUe
ErasmusMC
Generade
LUMC
Leiden University
Naturalis
TUDelft
AMC
AMOLF
CWI
NLeSC
NKI
SURFSARA
University of Amsterdam
VU University Amsterdam
VUMC
TNO
20
17
44
13 115
6
4
5
1
9Technology & data
‘hotels’
■ Access to high-tech
expertise & facilities
■ Wetlab & data facilities
■ Public and private labs
■ Training & education
High-quality
■ experimental design
■ measuring
■ data stewardship
ELIXIR: Data infrastructure for Europe’s life-science research
www.elixir-europe.org@ELIXIREurope
Data
Interoperability
Tools
Compute
Training
Marine metagenomics
Human data
Crop and forest plants
Rare diseases
data for life!
ELIXIR-NL Areas
Data Interoperability
e-Infrastructure services
Training & Education
NL data resources
Cross-RI collaboration
ESFRI-NL
e-Infra’s (via SURF)
Industry involvement
ELIXIR links data …
Expertise
Resources
(databases)
Compute & storage
Tools
Standards
Training
NL-NODE IN ELIXIR (‘DATA FOR LIFE’)
Technologies
Data
Learning
SCIENTIFIC DATA MUST BE FAIR
DTL INSTRUMENTAL IN DRIVING FAIR DEVELOPMENT
Findable
Accessible*
Interoperable
Re-usable
…… for both people and computers
*) NB: accessible ≠ open!
(e.g. proprietary data, privacy-sensitive data)
FAIR DATA PRINCIPLES PUBLISHED
Wilkinson et al. 2016 Nature Scientific Data
doi:10.1038/sdata.2016.18
EUROPEAN OPEN SCIENCE CLOUD (EOSC)
GLOBAL OPEN FAIR IMPLEMENTATION
WWW.GO-FAIR.ORG
As of 1 January 2018, five consortia are in the
process of becoming an Implementation
Network (Preparatory INs):
Metabolomics IN
Training IN
Personal Health Train IN
Rare disease IN
Biodiversity IN
FAIR METRICS
11-4-2018 11
Health-RI: The Dutch infrastructure for personalized health research
Health-RI will build on existing infrastructures and attract new partners
Network Health-RI
Health-RI ecosystem
Health-RI organization
inclusive network
>70 stakeholders
?
?
Initiatives converge
12
D4LS WP9: Access to Expertise
DATA Desk
DATA Desk
DATA Desk
DATA Desk
DATA Desk
DATA Desk
DATA Desk
DATA Desk
coordinationstandardstraining
big datadata stewardshipdata integration
Rob Hooft DTL
FAIR Tooling developed at DTL
● FAIR Data Interest Group● Data Stewards Interest Group
● Carpentries-nl Interest Group● Galaxy Interest Group
● NGS Interest Group
● Programmers Meeting● Compute Resources for LS
Research Interest Group
Training and community efforts
● FAIR Data● Data Stewardship
● Software and Data Carpentry● Galaxy
● Next Generation Sequencing
● Infrastructure
● Bioinformatics, System Biology, Metabolomics
Combining forces to provide data – related training
for the life science research community
COURSES, WORKSHOPS, FOCUS MEETINGS, HACKATHONS, …
■ Interest/Working Group meetings
■ Connecting virtual research environments and large scale computer resources (DTL/SURF SIG)
■ Dutch Galaxy working group: national agenda
towards Galaxy infrastructure and trainingwww.choosegalaxy.nl
■ Data Stewards Interest Group
■ Next Generation Sequencing Interest Group
■ Focus meetings: shaping solutions around a
common challenge
■ Creating a Bioinformatics and Data Stewardship Service Center
■ FAIR Tooling
Upcoming: Electronic Data Capture
COURSES, WORKSHOPS, FOCUS MEETINGS, HACKATHONS, …
■ Bi-monthly Programmers Meetings
■ Full Friday, introductions & hands-on
■ Average 25-30 attendents (30% industry)
■ Programmers subscribe to the programming-
interest mailing list (189)!
■ Software and data carpentry
■ Carpentries-nl mailing list
■ SWC/DC Instructor trainings
■ SWC/DC workshops for researchers
■ Building NL pool of SWC/DC instructors
■ Align with ELIXIR Europe SWC/DC project
22 June 2018: Building complex pipelines with Docker containers
FAIR Data Training activities
● ZonMw ETH FAIR Data Training
● ELIXIR Implementation Study:
Towards Data Stewardship in ELIXIR: Training &
Portal
● Bring Your Own Data Workshops (BYOD)
● Findability of courses – TeSS
4TH ETH CALL:
160 PROPOSALS, 60 JUST GOT SELECTED2018: FAIR TRAINING OF 60 PROJECT TEAMS
FAIR Data Training for Enabling Technology Hotels
Project
Target audience:
● technology hotel managers
● researchers awarded in ETH call
Goals:
● increased awareness of FAIR Data Principles
● making participating project more FAIR
● improved quality of Data Management Plans
Approach:
● A FAIR afternoon: on FAIR data stewardship for Technology
Hotel (/ETH4) beneficiaries, March 26 2018
● 5 separate hands-on workshops on FAIRification,
FAIR Data Training for Enabling Technology Hotels
Project
Hands-on tutorials:
● Q2/Q3 2018
● Single day
● 1 for each of 5 themes:
Genomics, Proteomics & Structural Biology,
Metabolomics, Bioimaging, Phenotyping and Medical
Imaging, Bioinformatics & Systems Biology
● ~ 25 participants
● Hosted by the hotels● Groningen will host one!
FAIR Data Training for Enabling Technology Hotels
Project
Participants will:
● Work with real-world dataset relevant to project theme
● Understand FAIR metrics and apply them to different
data resources
● Understand steps necessary in FAIRification process
● Identify and apply relevant ontologies
● Annotate datasets with appropriate metadata
● Learn about the FAIR tools and resources available● be ready to assess FAIRness of the data generated in the
project and have a concrete plan for next steps
Bring Your Own Data Workshop - BYOD
■ The main goal of these three-day events is to improve the
FAIRness of your data using linked data technology, and
learn how to combine your data with other FAIR datasets to
answer a scientific question.
■ Participants:
■ Data owners – specialists on given datasets
■ FAIR Data experts
■ Domain experts
■ Combination of hackaton & learning
■ Since 2014
■ https://www.dtls.nl/fair-data/byod/
Data Stewardship Support tree (Rob Hooft, DTL)
http://dmp.fairdata.solutions/
Towards Data Stewardship in ELIXIR: Training and
Portal (ELIXIR-NL, ELIXIR-LU, ELIXIR-CZ)
ELIXIR TRAINING PORTAL TeSS
• Platform to disseminate and discover training trainingmaterials and events
• Aggregating information from 46 content providers (ELIXIR nodes and various 3rd-party content providers) of which 21 are automatically aggregated
Feb 2018:
• 292 Upcoming Events
• >7000 past events• 803 Materials• 45 Providers
• https://tess.elixir-europe.org/
TeSS & ELIXIR-NL
https://www.dtls.nl/courses/
All Dutch courses in DTL course overview are automatically scraped and put in TeSS!Future plans: Bioschemas
FAIR Data Training activities (cntnd)
● Workshops & courses:
● FAIR Data Stewardship workshop for DTL partners Nov 2016
● BioSB Course Managing and Integrating Life Science
Information, Dec 2015 and Jan2018 (Marco Roos, Katy
Wolstencroft)
● FAIR session @ Lygature Partner meetup (2016, 2017)
● ‘FAIR Data and Data Stewardship in ELIXIR: How to write your
own FAIRy tale, ELIXIR AHM Rome, March 2017
● Training for HRB Ireland. Videos captured and available
● Workshop FAIR Training at ELIXIR AHM Berlin, June 2018
FAIR Data Training activities (cntnd) -
GO-FAIR & GO-TRAIN
● Participation in emerging GO-TRAIN implementation network
● “Paris group” Feb 2017 & Leiden Jan 2018
● Partners CODAT-RDA, ELIXIR, DTL, GOBLET, DCC, EDISON, LIBER,
DANS, SWC/DC
● Report The Objectives, Scope and Activities of a Possible GO
TRAIN Implementation Network
https://zenodo.org/record/1168504.
● Focal points:
● Train the trainer
● Training Framework
● Certification
● The Big Book of FAIRification – work in progress Erik Schultes
Mateusz Kuzak
FAIR Data Training activities (cntnd)
● Acquisition
● Interreg proposal Vlaanderen – Zuid Nederland.Training in Data Analysis & Stewardship (2018-2021)
● INFRAEOSC-4 (ELIXIR-NL together with BBMRI-NL, submitted March 2018)
● EJP Rare Disease, several NL partners
(to be submitted April 2018)
● Skills & competencies:
● ELIXIR Implementation Study Learning Paths
● Discussion with HBO/ DAS : defining data steward profession
● Working with EDISON, EOSCHub etc
● Collaboration with Elsevier: webinar Rob Hooft, DM fact
sheets
● https://www.dtls.nl/fair-data/fair-data-training/
ACKNOWLEDGEMENTS
● All DTL and ELIXIR-NL partners
● ZonMw
● ELIXIR
● DTL Core Team
● Merlijn van Rijswijk, Manager DTL Technologies
● Rob Hooft, Manager DTL Data
● DTL FAIR Engineering & BYOD Teams