Month: July 2015

Accessing health and health-related data: report from the Council of Canadian Academies

Canada is investing a lot of effort and resources into its healthcare system. To ensure that it provides the best possible care, high quality research data must be regularly fed into the system. Much of the data relevant to health research arise from interactions within the health system — every encounter with a physician, a pharmacist, a laboratory technician, or hospital staff generates data. The amount of data has grown significanly in the last several years. Due to the advances in information technolody, there are multpile ways to manage health and health-related data. Understanding the best ways to access, store, and govern these data is an important issue for Canada and Canadians. In 2013, the Canadian Institutes of Health Research (CIHR) asked the Council of Canadian Academies to answer the following question: What is the current state of knowledge surrounding timely access to health and social data for health research and health system innovation in Canada? The Panel of Canadian experts examined the technological and methodological challenges of accessing data; the benefits and risks of such access; legal and ethical considerations; and best practices for governance mechanisms that enable access. This report provides a foundation of knowledge that will support […]

symposium

DNAdigest symposium: incentives for data sharing – London, 21/08/2015

A medical doctor may be inspired to help people recover from injury and disease, a scientific researcher may be inspired by the opportunity to provide new insights to the world, but in their daily work what inspires the activities of a researcher? Many voices in the research community are talking about what the best practices for efficient and ethical data sharing should be in order to enable reproducible research, more reliable results, and faster diagnostics. But what use is the identification of best practices if we do not know what incentives will drive the research community to adopt them? Register for the DNAdigest symposium – August 21 from 9:30am at 3rd floor Shropshire House, 10-12 Capper Street, London At this DNAdigest symposium, we are inviting researchers, clinicians, patients, policy makers and the medical genomics community to discuss:  “How can we incentivise best practices for data sharing in genomics?”  The agenda will contain presentations giving different perspectives on data sharing and incentives, including presentations from Wellcome Trust (the largest research funder in the UK), bioethicists, data citation experts, and from the individual researchers. — SCHEDULE — 9:30 Arrivals (Tea/coffee is available) 9:45-10:00 Introduction to DNAdigest and the outline for the day Part I “Multiple perspectives on data […]

DNAdigest interviews ELIXIR

This week we are interviewing Niklas Blomberg from the ELIXIR project. 1. Please provide a short introduction to the work of ELIXIR? What are the aims and the mission of the project? ELIXIR is Europe’s response to the challenges of big data in life science research. Over the recent years, the amount of data produced by life science experiments increased exponentially and it has been estimated that by 2020 these data will be generated at up to one million times the current rate. ELIXIR’s goal is to orchestrate the collection, quality control and archiving of these data across Europe. For the first time, ELIXIR is creating an infrastructure that integrates research data from all corners of Europe and ensures a seamless service provision that is easily accessible to all.  ELIXIR’s services – biological data resources, tools, infrastructure, standards, compute and training – will benefit not only bioinformaticians and computational biologists, but also geneticists, biochemists, clinical specialists, and plant, environmental and marine scientists, both in academia and industry. 2. What does ELIXIR’s structure and legal framework look like? Rather than concentrating all of the expertise and resources in one place, ELIXIR has a distributed structure based on a hub and nodes […]

“Governance of data access” – a brand new report from EAGDA

The Expert Advisory Group on Data Access (EAGDA). Research funders are generally interested in maximising the value from the datasets generated by research, as well as in improving data management and accessibility practices. At the moment, many UK funders are actively working together to harmonise their research data policies. The Expert Advisory Group on Data Access (EAGDA) was established in 2012 by the Wellcome Trust, Cancer Research UK, the Economic and Social Research Council, and the Medical Research Council to provide strategic advice to these funders on the emerging scientific, legal and ethical issues associated with data access for human genetics research and cohort studies. EAGDA supports current and future studies and also seeks to enhance the UK’s input into international policy discussions on data access. Research data can often be highly valuable for use beyond the original study in which it was collected, and there has been a recent shift among funders, policy makers, publishers and the research community towards encouraging and enabling the sharing of research data with secondary users. A key challenge for researchers producing these datasets is in ensuring that the right balance can be struck between protecting the rights and interests of research participants, and maximising the […]

DNAdigest interviews the open study “Genes for Good”

Scott Vrieze, External Collaborator at Genes for Good 1. What is Genes for Good? Genes for Good is a research study led by Dr. Goncalo Abecasis at the University of Michigan, with the goal of discovering genes that affect risk for physical and mental health. Making these discoveries benefits from very large numbers of participants who are continually engaged with the study over time. To do this, we have created a Facebook App (apps.facebook.com/ genesforgood) where individuals may sign up, answer questions about their health and habits, and provide a saliva sample. DNA in the saliva will then be genotyped and tested for association with the health information. This kind of study has been quite successful in finding risk genes for a wide variety of diseases, and Genes for Good will continue this tradition, hopefully on a larger scale with many tens of thousands of participants.   2. What is your role in the Genes for Good study and how does your professional background fit? Genes for Good is intended to be an open platform. Researchers who are interested in contributing can very easily do so. I am a clinical psychologist interested in mental health issues like depression, anxiety, and […]

sharing

The Sharers’ Leaderboard: an h-index for data sharing

The idea for this guest post by Kate Hodesdon of Seven Bridges Genomics grew out of a discussion with Adam Resnick (Children’s Hospital of Philadelphia) and Deniz Kural (Seven Bridges Genomics). There is widespread recognition that sharing data benefits science. In this article, I’ll examine the best practices of data sharing, and assess the prospects for codifying these into a metric for how well scientists share data. When scientists say that sharing data is good for science, they have certain models of sharing and certain kinds of data in mind. I want to look at what makes someone a good sharer of data. For instance, simply being a prolific sharer is useless if the quality or relevance of the data is poor. And sharing high-quality data is not helpful if it you store it in an insecure repository, or an obscure format. Clarifying best practices of data sharing will help us maximize the value of shared data, but it can also play another important role of helping to incentivize data sharing. The problem of incentivization is that while data sharing undoubtedly benefits scientific progress, it is only beneficial to individuals if they can take advantage of another’s shared data. In […]

The Hyve

Open Source Technologies for Precision Medicine

The Hyve is a 30 person open source bioinformatics services company from Utrecht, Netherlands, and Cambridge, MA, USA. DNAdigest invited them to write a blog post on the summit “Open Source Technologies for Precision Medicine” that they organised in the beginning of June 2015 together with a life science consultancy Proventa International. The summit “Open Source Technologies for Precision Medicine” took place in London on June 03 and had good attendance from both industry and academia. The round table discussions and the panel discussion lead by Keith Elliston (CEO, tranSMART Foundation), John Wise (Executive Director, Pistoia Alliance), Paul Avillach (Assistant Professor, Harvard Medical School), Jay Bergeron (Director Translational & Bioinformatics, Pfizer), Gerrit Meijer (Professor, Netherlands Cancer Institute) and Kees van Bochove (CEO, The Hyve) resulted in some constructive conclusions about the current situation with open source as a means to achieve precision medicine. The main conclusions from the meeting: The ultimate business driver for adopting open source technologies such as tranSMART and cBioPortal seems to be access to data. For pharma IT, this especially means easy access to data from academics and non-profits, as well as annotated public studies and studies from (public-private) collaborations. Of course there is also the […]

BioData World Congress 2015

Get to know the speakers of the BioData World Congress: Ruth Chadwick

Genomics, big data and bioinformatics mark the start of the journey, personalised medicine is the end goal. How we get there will depend on whether we can get useable intelligence from the data – and then act on it. Held with the support of the Babraham Institute, BIA, BioNow, the Pharmacogenetics, Stratified Medicine Network and the Pistoia Alliance, BioData World Congress will:  examine the science and technology that is shaping and revolutionising our understanding of complex biological processes  review the game changing innovation, roadblocks and critical success factors in the utilisation of genomic data in personalised medicine  highlight how big data is driving developments in medical research  bring senior scientists within academia, pharma and biotech companies in order to facilitate discussion and partnerships This event is where innovation and expertise are showcased, solutions are found, and learning done. Join the world leading life science research institutions at BioData World Congress and help make personalised healthcare a reality. One of the official speakers at the event agreed to share a few words about herself and her thoughts on the congress. Please be introduced to Ruth Chadwick, Professor of Bioethics at the University of Manchester and a keen advocate of integrated care. Take […]

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