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Newsletter - February 2016

Vision 2016: connecting partner facilities and FAIR data
Two years ago, DTL was launched as a platform to bring together technology communities and infrastructures in the Dutch life sciences, with biomedical, agro, nutrition and biotechnology as application fields. Since then over 35 partners have joined the partnership to realise DTL’s mission: a connected infrastructure that allows data-intensive research crossing institute, sector and discipline boundaries. Today, 100 expert groups have registered their facilities as accessible technology ‘hotels’ specialised in multi-omics, bioimaging, bioinformatics,modelling or e-science, and DTL as the coordinator of ELIXIR-NL has pushed successfully to make data FAIR (Findable, Accessible, Interoperable and Reusable) for computers. This strategy is picked up widely and will become part and parcel of (international) data stewardship policies.

With its growing cross-sector and cross-disciplinary partnership, hotel-capacities, ELIXIR-connection, FAIR data successes and key infrastructure initiatives (see below), the DTL partnership has come to a stage where ambitions can now materialise into successes. In order to strengthen the scientific strategy of creating a coherent framework of collaborating and connected labs, three lead scientists have been appointed for the DTL programmes Data, Technologies and Learning: Barend Mons (LUMC), Alain van Gool (Radboudumc, TNO) and Jaap Heringa (VU). This team will be a great support for Rob Hooft, Merlijn van Rijswijk and Celia van Gelder as managers of the activities in the respective programmes. In 2016, there will be a focus on consolidating the connection between high-quality partner facilities and courses, and helping DTL partners to make their data FAIR and accessible for cross-disciplinary studies.

Vision 2025: large connected infrastructure for NL health research
Together, BBMRI-NL, EATRIS-NL and DTL/ELIXIR-NL worked out a vision and roadmap to create an infrastructure for research into medicine and health in the coming decade. We propose to bundle a wide range of distributed resources (biobanks, facilities, data collections) in a common large-scale infrastructure: Health-RI. For DTL, Health-RI provides an important spot on the horizon to direct its programmes in the coming years, in close collaboration with other communities. The broad DTL partnership will be... Read more

ELIXIR & FAIR Data

ELIXIR All hands meeting in Barcelona

On 7-10 March 2016 the ELIXIR Hub organises the second All Hands meeting, in Barcelona, It is an opportunity for members of the ELIXIR community from across the ELIXIR Nodes to meet and exchange views. Registration closes Feb 14th, 2016 Please contact Mascha Jansen if you want to attend the meeting, so we can coordinate the ELIXIR-NL representation.
Submit an abstract for ELIXIR NL/ISBE track at BioSB 2016

ELIXIR Netherlands will organise a technology /applications track at the BioSB 2016 conference (19 & 20 April). The track features four sessions: one session will be used to present the latest updates from ELIXIR-NL and ISBE, the other sessions are open for abstract submission. Please submit your abstract via the submission page and register for BioSB 2016.
ELIXIR partners with DTL and BioSB in organising ECCB2016

ELIXIR becomes the co-organising sponsor of the 15th European Conference on Computational Biology (ECCB), to take place on 3-7 September 2016 in The Hague. As part of the ECCB2016-ELIXIR partnership, the conference will feature a dedicated track to showcase ELIXIR activities and services. “We are delighted to have ELIXIR as a strong partner”, says Jaap Heringa, Chair of the ECCB 2016 Organising committee. “As one of the major initiatives in Europe and globally, we are happy to give ELIXIR a venue to present their... Read more
Personal Health Train launched through first projects

The Personal Health Train (PHT) initiative aims for increased utilization of existing biomedical data. The key concept behind the PHT is to bring research to the data rather than the classical solution of bringing data to the research. The PHT initiative invites partners to jump on the train and make the PHT a reality through collaboration and by jointly acquiring funding. Two such collaborative projects were recently granted, one in a call from COMMIT and the other
as part of the STW Perspectief programme.
Kick-off EXCELERATE training subtasks

On 19 – 21 January 2016, two ELIXIR-EXCELERATE training platform subtasks – Training the trainer and Ensuring impact and quality, officially kicked-off with a joint workshop. For more information on the participation from ELIXIR-NL, please contact Celia van Gelder, co-lead European training platform. Read more
FAIR Data Points as EUDAT services

DTL will participate in a pilot project to evaluate FAIR Data Points as new EUDAT services helping data owners to make their datasets available in a FAIR way. A FAIR Data Point (FDP) is software that allows: (1) data owners to expose datasets in a FAIR manner and (2) data users to discover information about the offered datasets and, if license conditions allow... Read more
FAIRDOMHub systems biology commons is open!

FAIRDOMHub is a centrally hosted repository for managing and sharing systems biology research. It enables independent researchers, projects and programmes to manage or publish datasets, link them together, interlink them with mathematical models, and share them in the context of the protocols that produced them and the publications that describe them. FAIRDOM therefore... Read more
ELIXIR launches F1000 research publication channel

Last December ELIXIR announced the launch of the ELIXIR F1000Research Gateway to publish its research and technical outputs. The ELIXIR Gateway is a collaboration between ELIXIR and the F1000 Research open science publication platform, please see the Editorial. Niklas Blomberg, director of ELIXIR: “Rapid, transparent communication of our efforts to the wider research community is critical to ELIXIR success and so we are delighted to... Read more
DTL Data programme & ELIXIR-NL If you have a question about the DTL Data programme and/or ELIXIR-NL, please contact Rob Hooft.

Technology facilities 


DTL/MGC Technologies facilities course well received
On January 18-12 Medical Genetics Centre “South-West Holland” and DTL jointly organised a four day course on Technology Facilities. Over 35 participants (MSc or Postdoc level) learned how to apply proteomics, genomics, medical imaging and metabolomics in biomedical research. "At the request of DTL, a full day of... Read more

DTL Technologies' focus meetings
Two focus meetings related to the DTL Technologies programme are planned: a focus meeting on scalability of image storage and processing on February 29, and a meeting on FAIR data stewardship and Data management plans for DTL Hotel managers on March 22, 2016. Please find more information in the meetings & events section of this newsletter.

DTL Technologies programme
If you have a question regarding the DTL Technologies programme, or if you'd like your facility to be included in the overview on the DTL website, please contact Merlijn van Rijswijk.

Training & Outreach

Succesful first edition of "Essential Skills in Data-Intensive Research” course
From 25-29 January the first edition of the “Essential Skills in Data-Intensive Research” course took place in Utrecht. This training is a collaborative effort of the Netherlands eScience Center, SURFsara, DTL, VU University Amsterdam and the Software and Data Carpentry foundation. The heavily oversubscribed course attracted around 30 participants from across the Netherlands. This training was the first of its kind, with... Read more

Upcoming BioSB courses – Save the date!
BioSB has started to fill the course portfolio for 2016. Two courses that already have been planned are: Registration for these courses will be open soon. However, you can pre-register, in which case you will be notified once the registration is open.

GOBLET’S train the trainer workshop
In November 2015, GOBLET organised a two day Train the trainer workshop in Cape Town, South Africa. When developing a new course or curriculum, it’s extremely helpful to have some pointers as to what bioinformatics competencies scientists in different roles might realistically have. Celia van Gelder (representing the ELIXIR Training platform) was one of the speakers who presented examples of how competency profiles... Read more

DTL Course Directory – present your courses to the DTL community!
You can find an overview of courses in the DTL Course Directory. We can only build the DTL Course Directory with your help, so please take a moment to publish your course(s) using the Course Submission Form. Courses of DTL Partners will also be presented on their particular partner page.

DTL Learning programme & Outreach
If you have a question about the DTL Learning programme and/or outreach activities,please contact Celia van Gelder.

Meetings & events

Opening calls for ECCB 2016
On 3-7 September 2016 DTL, the BioSB research school and ELIXIR will jointly organise the fifteenth edition of the European Conference on Computational Biology (ECCB2016)in the Hague. You are invited to submit an abstract or paper for the following calls: Proceedings, Highlights, Applications, ELIXIR Applications and Posters. More information on the preliminary programme is available as well.

DTL Focus meeting: scalability of image storage and processing
Modern multicenter imaging studies may easily generate hundreds of terabytes of raw and processed image data for quantitative analyses. How can we in the imaging community ensure good data stewardship? The next DTL Focus meeting (29 February, 2016, SURF) focuses on this question. The meeting is an excellent opportunity to learn more about the latest developments in FAIR data stewardship and hear firsthand experiences from collegues in the Dutch imaging community. Speakers include Jason Swedlow (University of Dundee), Wiro Niessen & Erik Meijering (Erasmus MC), and Jose Guerra (Enza seeds). Read more

DTL Focus meeting: Fair data stewardship and Data management plans for DTL Hotel managers
On 22 March, 2016 the DTL Technologies programme organises a focus meeting for its Hotel managers. DTL Technology Hotels are frequently asked to practice FAIR Data stewardship, either because of internal requirements or by funding organizations like ZonMw and NWO. This focus meeting is an excellent opportunity to meet other Technology Hotel managers and to learn more about the latest developments in FAIR data stewardship. Speakers include Gabino Sanchez Perez (PRI Wageningen), Thomas Hankemeier (Leiden University) and Rob Hooft (DTL). Read more

DTL Interest Group on Next Generation Sequencing
DTL recently started a Next Generation Sequencing Interest Group, bringing together researchers and bioinformaticians that work with NGS data. The main aim of the NGS Interest Group is to share best practices and foster future collaborations.The Interest group will regularly organise meetings about different subjects.If you’re interested in joining the NGS Interest group, please contact Leon Mei. Read more

DTL Programmers meetings
To encourage collaboration and communication between scientific programmers active in the Dutch life sciences field, DTL organises regular programmers meetings. Subjects of the lectures and workshops range from new developments in programming languages through practical tips and tricks to direct life science applications.Anyone interested can join the programmers meetings. For more information please contact Rob Hooft.

Partner news


DTL partner ENPICOM announces its new two-day course "Python for life scientists" the first part of the series "From Zero to Hero", tailored for life scientists with little or no prior programming experience. The course is driven by real-life use cases, taking participants from the basics up to drawing a volcano plot. Participants will learn... Read more

Dr. ir. Natal van Riel has been appointed as professor of Computational Modelling at DTL partner University of Amsterdam‘s Faculty of Medicine (AMC-UvA).Van Riel conducts research on the development and application of computer models for metabolism and metabolic networks. As part of his appointment at the AMC-UvA, Van Riel will develop his computer models... Read more

DTL Partner Euretos has expanded the coverage of their Euretos Knowledge platform to include 65 major public life sciences data and publication sources. The company has significantly accelerated the ability to add new data sources and expects to hit the 100-sources mark in the first quarter of 2016. “It is the combination of the scope of our knowledge base, together with... Read more

Maurice Verheesen of DTL partner AT Computing recently wrote two news items about ways in which AT Computing can support computational job scheduling and configuration management. Please contact Maurice for more information.

Since April 2015, DTL partner Elsevier offers a free and open online training platform for all researchers or training partners in academia: the Elsevier Publishing Campus. The Campus supports researchers at the start of their academic career right through becoming a journal editor / teacher themselves. Read more

Last December DTL partner Wageningen UR's Bioinformatics department announced that NWO Groen granted two of their applications. The projects “Harnessing the soil microbiome for improved stress tolerance in crop plants” (Marnix Medema) and “Exploitation of Copy Number Variation for rapid improvement of abiotic stress tolerance in crops” (Mark Aarts, co-applicant Dick de Ridder) will receive funding.

DTL partner BaseClear collaborates in consortium to investigate aquatic biodiversity. Theconsortium is working within TKI Water Technology to develop and make available DNA techniques for the monitoring of biodiversity. “Thanks to DNA techniques we can determine, in a routine and reliable manner, the species that are present in water samples. We make... Read more

Recently, SURFdrive of DTL partner SURF released three video tutorials designed to answer practical questions on the SURFdrive web environment, on sharing files and folders and on synchronising with the SURFdrive client. SURFdrive is a personal cloud storage service for... Read more
Your news announced on the DTL website & in the newsletter
If your organisation is one of the DTL Partners, you can announce your news through the DTL website. Please send your news items to Mascha Jansen.

Overview courses & events
 

Courses
  • Successful planning of large data generating experiments, 16 March 2016, Leuven, Belgium Read more
  • Bayesiaanse statistiek cursus, 18 March 2016, Amsterdam Read more
  • Introduction to next generation sequencing; technologies, applictions and data analysis, 12-15 April 2016, Breda Read more
  • In silico life: constraint-based modelling at genome scale, 9-11 May 2016, Amsterdam Read more
  • Python for life scientists, 13-14 May 2016, Amsterdam Read more
  • Algorithms for biological networks (4th edition), 23-27 May 2016, Delft Read more
  • Evolutionary genomics, 23 May - 3 June, Utrecht Read more
  • XNAT workshop, 6-10 June, 2016, St. Louis, Missouri, USA Read more
  • Metabolomics for microbial systems biology, 11-15 July 2016, Delft Read more
  • International data week (IDW), 11-17 September 2016, Denver, Colorado, USA Read more
  • Genomics in industrial biotechnology, 31 October - 4 November 2016, Delft Read more
Events
  • Systems Medicine: Understanding disease pathways for personalised treatment, 15 February 2016, Utrecht Read more
  • Linking life science data: design to implementation, and beyond, 18 February 2016, Vienna, Austria Read more
  • DTL focus meeting: 'Scalability of image storage and processing', 29 February 2016, Utrecht Read more
  • ZONMW / NFU-Data4Lifesciences meeting, 1 March 2016, Utrecht Read more
  • DTL focus meeting: 'New sequencing technology: Nanopore and Pacbio', 8 March 2016, Utrecht Read more
  • 3rd Embo conference on visualizing biological data (VIZBI 2016), 9 March 2016, Heidelberg, Germany Read more
  • Bytemal Conference, 9 March 2016, Maastricht Read more
  • Successful planning of large data generating experiments, 16 March 2016, Leuven, Belgium, Read more
  • Applied bioinformatics in life sciences, 17 March 2016, Leuven, Belgium Read more
  • DTL focus meeting: 'Fair data stewardship and data management plans for DTL hotel managers', 22 March 2016, Utrecht Read more
  • BIOSB 2016: Dutch bioinformatics @ systems biology conference, 19 April 2016, Lunteren Read more
  • CTLS 2016 - Core technologies for life sciences, 12 June 2016, Heidelberg, Germany Read more
  • ECCB 2016 – 15th European Conference on Computational Biology, 3-7 September 2016, The Hague Read more
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