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