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Newsletter - February 2017

Interview: On data challenges in agricultural science


Dr Ernst van den Ende and Dr Richard Finkers of Wageningen UR are on top of the recent developments in the field of agricultural science. "Growing enough food sustainably for the expanding world population presents a formidable challenge. We will need sophisticated data handling techniques to face this challenge," says Van den Ende.
 
Van den Ende is the Director of the Plant Sciences Group at Wageningen University and Research and a member of the DTL Board. He explains: “In the 20th century, plant breeding techniques, artificial fertilizers, and pesticides drove green revolutions in the sense that we achieved higher yields in important crops. In recent years, many high-end technologies have been introduced in our field. For instance, omics techniques such as genomics and metabolomics are now used to characterise crop genotypes and phenotypes. And sophisticated sensors, drones, and satellites provide valuable information about, for example, climate, soil characteristics, and break-outs of infectious diseases. I think that these data will drive the next green revolution.
 
Precision agriculture
The high-end technologies have resulted in the emergence of precision agriculture. This is the green counterpart of precision medicine, where a doctor chooses an optimal treatment based on a combination of data sources (e.g., a DNA test and clinical data). In precision agriculture, a farmer chooses an optimal farming strategy based on a combination of data (e.g., omics data and soil characteristics measured with sensors). Applications of precision agriculture are already available. For instance, meteorological information and data on soil conditions are linked in systems that warn farmers against break-outs of infectious diseases.
Read more.

FAIR data and Open Science

 
Find FAIR data knowledge and expertise
The DTL website now features a list of FAIR data knowledge and expertise. Have a look!
 
Open science in Ireland
In January, the DTL FAIR Data team delivered a FAIR data workshop at the Irish Health Research Board (HRB) in Dublin. “As one of the major research funders in Ireland, we value research data as an important output of scientific research. But we do not have deep knowledge about data stewardship. We learned that the Dutch team has conducted a lot of research on this topic and developed prototypical solutions and training materials. So, we asked them to come and explain the FAIR data principles to our stakeholders,” says Dr Annalisa Montesanti, programme manager at HRB. Read more.
 
National Plan Open Science presented
On 9 February, the National Plan Open Science was launched in The Hague. The plan lists the current activities and ambitions of Dutch organisations that intend to take action to make science more open. Read more.
 
GO FAIR and the European Open Science Cloud
In 2016, the European Commission launched the European Open Science Cloud (EOSC). Now, a group of 'early mover' EU member states is preparing the GO FAIR initiative, which is a proposal for the practical implementation of the EOSC. GO FAIR is led by Professor Barend Mons (DTL) and Professor Erik Fledderus (SURF). Read more.
 
Hackathons
DTL has organised several FAIR hackathons in the past few months. Where Bring Your Own Data workshops focus on making data FAIR, FAIR hackathons have the purpose of making tools FAIR. Read the reports about the Quaero Systems and Castor hackathons to find out more.
 
  Please contact Mascha Jansen to learn more about FAIR data activities.

ELIXIR

 
ELIXIR Belgium launched
The Belgian node of ELIXIR was launched on 9 February. You can find pictures and slides of the presentations on the ELIXIR Belgium website.
 
  BioSchemas supports the discovery of public datasets
Google recently published guidelines for the discovery of science datasets that help data providers describe their datasets in a structured way. The published guidelines draw on the metadata specifications for life science datasets developed by BioSchemas. BioSchemas is an open community initiative driven by ELIXIR to improve interoperability of life science data. Read more.
 
 
Please contact Rob Hooft if you have a question about ELIXIR-NL.

Training and education

 
Education & Training activities at the NETTAB2016 conference: a short report
On 25 and 26 October 2016, the NETTAB2016 conference was organised in Rome. The theme was ‘Reproducibility, Standards and SOP in Bioinformatics. The conference also brought together people from all over Europe who are involved in training and the organisation of training. Read more.
 
Looking back on the first European Galaxy Developer Workshop
Galaxy is an open, web-based platform for data-intensive biomedical research. On 16-19 January 2017, the first European Galaxy Developer Workshop took place in Strasbourg. ELIXIR-NL and the Dutch Galaxy Working Group were actively involved in the workshop's organisation. Read more.
 
Please send us your courses
The DTL Course Overview provides a searchable overview of courses, trainings, and workshops in the field of data and technologies for the life sciences. The courses are automatically transferred to the European training portal TeSS. We need your help to fill the Course Directory, so please take a moment to fill out our Course Submission Form. We also welcome information about courses that are organised upon request or when there is sufficient interest. You can send your questions and suggestions to learning at dtls.nl.
 
  Please contact Celia van Gelder if you have questions about DTL/ELIXIR-NL training, education, and outreach activities.

DTL Varia

 
EUR 2.25 million for essential building block of Health-RI
The Dutch Cancer Society will fund the Translational Research IT (TraIT) project with EUR 2.25 million to build an integrated Dutch biomedical research infrastructure. Read more.
 
Inspiring BIUP company visit
On 27 January 2017, the BioInformatics Industrial User Platform (BIUP) organised a company visit to Genetwister in Wageningen. More than 20 participants from almost as many different companies involved in bioinformatics shared ideas on cloud computing, DTL, and bioinformatics for plant breeding. Read more.
 
New statistical method improves reproducibility of omics research
A novel Bayesian method to detect and correct for bias and inflation in epigenome- and transcriptome-wide association studies has been published. The method was developed within the framework of BBMRI-NL 2.0. Read more.
 

Upcoming meetings and events

 
24 February: inaugural lecture Dr Wessel Kraaij
You are invited to the inaugural lecture of Dr Wessel Kraaij, who has been appointed as a Professor in Applied Data Analytics at Leiden University. The lecture will take place on 24 February at 16:00. Read more.
 
9 March: DTL Focus Meeting
The meeting's theme is 'Don’t Reinvent the Wheel: Creating a Bioinformatics and Data Stewardship Service Center'. In this meeting, we would like to establish a dialogue among the bioinformaticians that are involved in setting up or managing a bioinformatics facility in order to learn from each other. Read more
 
9-10 March: workshop 'Establishing a node for FAIRifying metabolomics and phenomics data in the European Open Science Cloud'
This is a joint workshop of PhenoMeNal and the GO FAIR initiative. At the end of the workshop, we will launch one of the first nodes in the European Open Science Cloud, for FAIRifying metabolomics and phenomics data. Read more.
 
15 March: ‘Compute Resources for Life Science Research‘ meeting
The DTL/SURF Interest Group ‘Compute Resources for Life Science Research‘ will meet at SURF in Utrecht. Topic of the meeting will be ‘Reproducible pipelines – integration with software stack.’ Read more.
 
17 March: DTL Programmers Meeting
To encourage collaboration and communication between scientific programmers active in the Dutch life sciences field, DTL organises regular programmers meetings in collaboration with SURF. The next meeting is planned for 17 March 2017. The meeting's programme is still to be determined, so suggestions for topics are welcome.
 
22-23 March: Data Carpentry workshop 
The NLeSC and UMC Utrecht will organise a Data Carpentry workshop at the NLeSC in Amsterdam. The main target audience is researchers in the life sciences. More details will be announced on the DTL website soon.
 
30-31 March / 7 April: 'BBMRI-omics: Introduction and Hands-on Application'.
During the two day event, researchers can get acquainted with the data BBMRI-omics has on offer for the research community. Read more.
 
4-5 April: BioSB conference
The 3rd edition of the Bioinformatics and Systems Biology conference will be held on 4 and 5 April 2017 at the conference center De Werelt in Lunteren. The call for nominations for the BioSB Young Investigator Award 2017 is still open. More information can be found on the conference website.
 
7 April: National DNA lab day
Registration is now open for the 5th edition of the DNA-lab day on 7 April 2017 in the Reehorst in Ede. The day will feature many interesting workshops for Dutch high school teachers.
 
  A longer list of upcoming courses and events is available on the DTL website. Please contact Femke Francissen if you have a question about events.

Partner news

 
We warmly welcome two new DTL partners: Princess Máxima Center for Pediatric Oncology and Hartwig Medical Foundation. Read more about our partners on the DTL partner list and please contact Ruben Kok if you want information on how to become a DTL partner.
 
Huawei and SURFsara have announced a strategic partnership for stimulating ICT innovations in the fields of Smart Healthcare and Smart Energy that will benefit society and a sustainable economy. Read more.
 
DTL's new partner Hartwig Medical Foundation and national pathology network PALGA have announced a collaboration to improve oncological care. Read more.
 
Data computing is working on a ‘Personal Locker’, which is a decentralised open source, open hardware way of storing personal (health) data. Read more.
The World Wide Web Consortium has announced that it will join forces with the International Digital Publishing Forum to set up a new roadmap for Digital Publishing. Ivan Herman, researcher at CWI, has played a seminal role in this. Read more.
  If your organisation is a DTL Partner, you can announce your news, events, courses, and job vacancies on the DTL website. Please send these items to communication@dtls.nl.
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