Interview: Towards an international research data infrastructure for biodiversity and ecology studies
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Image: Researcher at Naturalis Biodiversity Center
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For centuries, scientists all over the world have established enormous collections of animals, plants, microbes, fossils, minerals, and rocks. The data associated with these specimens can help researchers understand life on earth, counter biodiversity loss, and contribute to a sustainable future. However, to arrive at new scientific insights and solutions for environmental problems, researchers should integrate data from various sources. “This is a formidable challenge because the data are scattered over the world and collections are often not digitised,” says Wouter Addink of Naturalis. Read more.
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FAIR data and Open Science
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Key role for Personal Health Train and FAIR in LSH Knowledge and Innovation Agenda
In August 2017, the Dutch Top Sector Life Sciences & Health (LSH) launched its Knowledge and Innovation Agenda 2018-2021. This strategic document describes LSH's health and care ambitions for the next four years. The agenda mentions that ‘many Dutch LSH highlights are famous worldwide, including the upcoming Dutch ICT-breakthrough innovation of the Personal Health Train that incorporates the FAIR principles adopted by the European Commission and G20.’ In addition, it announces that LSH will facilitate Health-RI, FAIRdICT, and GO FAIR.
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Looking back on two Bring Your Own Data workshops
DTL and ELIXIR-NL frequently organise Bring Your Own Data (BYOD) workshops, where experts assist you in making your research data FAIR. (Read more.)
On 30 May - 1 June 2017, ELIXIR Belgium and ELIXIR-NL organised a BYOD in Ghent. The event demonstrated the potential of FAIR data in plant research and featured a hackathon to make the interoperability platform within the plant domain (BrAPI) FAIR. Read a report of the event.
UMC Utrecht and DTL organised a cancer omics BYOD on 6-8 June 2017 in Utrecht. Four Cancer Genomics Center datasets were made FAIR and we demonstrated the advantages of interoperability. Read the report written by Daphne van Beek.
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ELIXIR publishes position paper on FAIR data management in life sciences
On 7 September 2017, ELIXIR stated how its infrastructure will help researchers to make published life science data FAIR. This statement also voices ELIXIR’s commitment to enabling the availability of FAIR data within the framework of the European Open Science Cloud. Read more.
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Nature editorials on Open Science and FAIR
In June 2017, two editorials related to Open Science and the FAIR principles were published. The Nature editorial Don’t let Europe’s open science dream drift' mentions the GO FAIR initiative and the Nature Genetics editorial Data models to GO FAIR calls for submissions containing linked open data models that embody and extend the FAIR principles.
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8 November: FAIR tooling Focus Meeting
DTL and SURF are preparing a Focus Meeting on FAIR tooling. Several Dutch groups are implementing the FAIR principles in data management tools. The Focus Meeting is a first attempt to coordinate and align these efforts. Join us on 8 November in Utrecht.
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The DTL website features a demo of FAIR Data tools, a list of FAIR data knowledge and expertise, a FAIR guide for publishing research data, general information on FAIR data, and an Events Calendar. Please contact Mascha Jansen for more information about our FAIR data activities and Rob Hooft for information about the DTL Data programme.
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Sneak preview Enabling Technologies Hotels Call response
The latest Enabling Technologies Hotels Call closed on 29 August 2017. Dr Sander Hougee, Programme Officer Life Sciences and Health at ZonMw, gives a sneak preview of the response to the call. Read more.
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The future of metabolomics and proteomics in ELIXIR
Representatives from the European metabolomics and proteomics communities have prepared proposals to integrate metabolomics and proteomics activities in ELIXIR. The teams have written two white papers that have been published as F1000 opinion articles. Read more.
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Biomarker conference on 6 October
The Biomarker Development Center organises a conference ‘Validation of Biomarkers – Bridging the innovation gap through integrated technologies’ on 6 October 2017 in De Doelen in Rotterdam. The organisers are Dr Theo Luider (ErasmusMC), Professor Rainer Bischoff (University of Groningen), Professor Ron Wevers (Radboudumc, Nijmegen), and Professor Alain van Gool (Radboudumc). Read more.
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Microbiome events
The 9-10 October ELIXIR Innovation and SME-forum on 'Data-Driven Innovation in Food, Nutrition and Microbiome' in Brussels will feature
- interactive sessions on Data Sources, Tools & Analysis, and Integration Challenges enabling microbiome research and innovation,
- showcases of free data resources and services available through ELIXIR,
- examples of companies that use public data in their business, such as MyMicroZoo and MS-Omics,
- training opportunities in this field.
The event is organised by ELIXIR Belgium. DTL's Merlijn van Rijswijk is a member of the organising committee. More information and registration.
The ELIXIR Innovation and SME-forum is followed by an international workshop 'Personalised nutrition for better health - targeting the microbiome' on 10-11 October. This event will take place at the same venue (the Brussels City Theatre). Dirk Gevers of the Janssen Microbiome Center (USA) will give a keynote presentation. Read more.
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The DTL website features a catalogue of 130+ Technology Hotels. These are expert groups that offer their high-end technologies, expertise, and infrastructure to researchers who do not have access to such facilities at their home institute. Please contact Merlijn van Rijswijk for more information about the DTL Technologies programme.
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BioSB: upcoming courses and evaluation report
The BioSB research school has a number of courses coming up. See the BioSB newsletter for further details. In April 2017, an international committee consisting of Boris Kholodenko, Emmanuel Barillot, and Terri Atwood reviewed BioSB's activities. The committee was highly positive and advised on how to transform BioSB into a vibrant and sustainable organisation. You can download the final report from the BioSB website.
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Amgen Foundation launches Amgen Biotech Experience in the Netherlands
In the next three years, the DNA Labs on the Road will collaborate with the Amgen Biotech Experience (ABE) to educate Dutch high school students about biotechnology. The DNA Labs on the Road are mobile practicals that educate high school students about DNA, genes, genomics, and the latest research techniques. In 2017, the DNA Labs received pilot funding from the ABE and the collaboration will now be prolonged. Read more.
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ELIXIR Training papers in F1000R channel
The ELIXIR Training Platform has published papers on two pilots in the ELIXIR F1000R channel. The Dutch node of ELIXIR has actively been involved in these two pilots.
ELIXIR-EXCELERATE Train-the-Trainer pilot: As a first step towards a pan-European training programme, a pilot was developed, drawing on existing ‘instructor training’ models, using input both from experienced instructors and from experts in bioinformatics, the cognitive sciences, and educational psychology. The F1000R paper describes the process of defining the pilot programme, illustrates its goals, structure and contents, and discusses its outcomes. Read more.
ELIXIR Software and Data Carpentry Pilot action: ELIXIR has adopted a well-established and progressive programme of computational lab and data skills training based on Software and Data Carpentry, aimed at increasing the number of skilled life scientists and building a sustainable training community in this field. The F1000R paper describes a Pilot action that introduced the Carpentry training model to the ELIXIR community. Read more.
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Two data courses in Belgium
ELIXIR Belgium will organise two training courses in the coming months: Python for data processing (5-6 October) and Fundamental data skills for data-driven research (6-7 November). More information and registration.
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The DTL course overview lists courses in the field of data and technologies for the life sciences. It is automatically transferred to ELIXIR's European training portal TeSS. Please contact Celia van Gelder if you want your training events and materials to be included or if you have questions about the DTL Learning programme.
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New partners
The latest addition to the DTL partnership is the company De research manager. "Our mission is to develop business solutions taking data collection and processing off the hands of researchers and healthcare specialists. We are ISO 27001 certified and fully specialised in data solutions for the healthcare sector," says Paul Somberg, CEO of de Research Manager.
In the June 2017 newsletter, we announced Agri Information Partners as our new partner. They would like to introduce themselves as well: "Agri Information Partners is an IT specialist for plant breeding companies, companies in the Agri & Food sector, and certification companies. We help these companies organise key processes in a more efficient, simpler, and smarter way by offering expert consultancy with knowledge of the primary processes. We help our clients by enabling them to use all information available to optimize decision making. This is done by offering hands-on advice and the realisation of integrated information systems," says Ad Ordelman, Commercial director of Agri Information Partners.
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New core team member
DTL is organised as a network of experts and policymakers affiliated with the DTL partners. This DTL network is supported by a small core team located in Utrecht. (Read more about the organisation.) Mateusz Kuzak has recently joined our core team as a scientific community manager. Mateusz: "I have been involved in the Dutch Bioinformatics community since my arrival in the Netherlands seven years ago. Since then, I have worked as a research software engineer at the University of Amsterdam and later as eScience Research Engineer at the Netherlands eScience Center. In addition, I have been involved in Software and Data Carpentry initiatives as an instructor, trainer, and steering committee member."
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Bioinformatics in the Netherlands
The scientific journal Briefings in Bioinformatics recently published a paper about the history of Bioinformatics in the Netherlands. The authors are affiliated to DTL, ELIXIR-NL, and BioSB and they describe the process of building the Dutch Bioinformatics community since 2003: from NBIC to DTL, ELIXIR-NL, and BioSB. Read the paper.
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ELIXIR publications
In the past few months, ELIXIR Europe has published or released
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Think BIG: Data for health
The Netherlands has unprecedented opportunities to exploit its strong position in big data research to improve healthcare and the well-being of citizens. That is the conclusion of the report ‘Think BIG: DATA for Health’, commissioned by Commit2Data. Read more.
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29 September: Programmers meeting
To encourage collaboration and communication between scientific programmers active in the Dutch life sciences field, DTL frequently organises programmers meetings in collaboration with SURF. The next meeting will take place on 29 September.
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8 December: Health-RI Conference
Please join us at the 3rd Health-RI Conference on 8 December 2017 in Utrecht. Health-RI aims to establish an interconnected data infrastructure for Dutch personalised medicine and health research. It is a joint initiative of DTL, ELIXIR-NL, BBMRI-NL, EATRIS-NL, NFU, and Health~Holland, supported by a large group of stakeholders in the health domain. Read more on the Health-RI website.
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DTL is a public-private partnership of more than 50 Dutch life science organisations. It acts as a network of professionals that jointly improve the Dutch life science research infrastructure. Contact Ruben Kok if your organisation wants to become a DTL parther and Rob Hooft if you have a question about ELIXIR-NL.
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The Dutch National eScience Symposium is a yearly one-day event where scientists from different disciplines meet to discover how digital technology impacts scientific practice. This year, it will take place on 12 October in the Amsterdam ArenA. The symposium will feature five thematic sessions showcasing world-class data-driven and compute-intensive research. For the Life science & eHealth track, the theme will be 'Brain, Cognition, and Behavior'. Read more.
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ENPICOM has announced the expansion of its team with the experienced Life Sciences industry executive and health-tech entrepreneur Jos Lunenberg. (Read the press release.) In addition, the company was recently featured in a GenomeWeb article, highlighting ENPICOM’s growing role in the immunotherapy-support space. You can read the full article here.
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Researchers from TNO have published a paper about Systems biology of personalised nutrition in the scientific journal 'Nutrition reviews'. Read the paper.
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The Bio-design and Modeling group of the DSM Biotechnology Center has a data scientist vacancy. Read more.
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In September 2017, Martijn Kersloot started his PhD programme at Castor EDC. Martijn will develop a scalable solution for standardising medical research data, both retrospective and prospective. Derk Arts (CEO of Castor EDC): “We invite the other DTL partners to contact us if they want to become involved in this project.” Castor has also announced that its dynamic consent platform ‘MyConsent’ is ready for the first pilots. Read more.
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DTL has moved into a new office on 1 July 2017. We are now located in the Jaarbeurs Innovation Mile (JIM), Jaarbeursplein 6, 3521 AL, Utrecht. Our new Postal address is Postbus 8500, 3503 RM, Utrecht. 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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