UK

Walking the talk – reflections on working ‘openly’

As part of Open Access Week 2016, the University of Cambridge Office of Scholarly Communication published a series of blog posts on open access and open research. In this post, Dr Lauren Cadwallader discusses her experience of researching openly. Earlier this year I was awarded the first Altmetric.com Annual Research grant to carry out a proof-of-concept study looking at using altmetrics as a way of identifying journal articles that eventually get included into a policy document. As part of the grant condition I am required to share this work openly. “No problem!” I thought, “My job is all about being open. I know exactly what to do.” However, it’s been several years since I last carried out an academic research project and my previous work was carried out with no idea of the concept of open research (although I’m now sharing lots of it here!). Throughout my project I kept a diary documenting my reflections on being open (and researching in general) – mainly the mistakes I made along the way and the lessons I learnt. This blog post summarises those lessons. To begin at the beginning I carried out a PhD at Cambridge not really aware of scholarly best practice. […]

DNAdigest interviews Personal Genome Project: UK

Today we begin the series of interviews about Personal Genome Projects and this interview is with Professor Stephan Beck who is leading Personal Genome Project: UK. Please introduce yourself. What is PGP in general and how is PGP-UK different? I am a Professor of Medical Genomics at the UCL Cancer Institute and the Director of Personal Genome Project: UK (PGP-UK). My academic group is involved in projects investigating genomics and epigenomics of phenotypic plasticity in health and disease. We are a systems epigenomics group that is interested broadly in all aspects of it. PGP-UK is a member of the Global PGP Network which currently includes four PGPs. The first one was founded by George Church in 2005 at Harvard University, then in 2012 Stephen Scherer started PGP-Canada in Toronto. In 2013, we launched PGP-UK at UCL. In 2014, PGP-Austria was launched by Christoph Bock in Vienna. These are the four projects that are currently active. There is a number of projects that are being planned and some of them are very close to actually launching as well but that will be announced when they are ready. What was the motivation to start the very first one? What was the aim […]

A new genome editing review from Nuffield Council on Bioethics

In September 2016, Nuffield Council on Bioethics presented Genome editing: an ethical review. The summary below is written by Jessica Cussins and is originally published here. Reposted with the author’s permission. 7 Highlights from Nuffield Council’s Review on the Ethics of Genome Editing Posted by Jessica Cussins, Biopolitical Times guest contributor on October 18th, 2016 The UK Nuffield Council on Bioethics’ recently released report, Genome Editing: an ethical review  (full version available here) is the most substantial and thorough assessment of its kind. It delves deeply into the ethical, social, and political underpinnings and implications of genome editing, and touches on related, converging technologies including synthetic biology, gene drives, and de-extinction. A second report with ethical guidance regarding the use of genome editing for human reproduction is due in early 2017 from a Council working group chaired by Karen Yeung. This first report will be an important reference for people across disciplines for some time, and I will not do justice to its scope and breadth here. However, I want to draw attention to just seven concepts that are particularly helpful and illuminating, as much for their framing of the questions at stake as for their content. I briefly summarize […]

DNAdigest interviews the Head of ELIXIR’s Human Genomics and Translational Data

Serena Scollen is the Head of Human Genomics and Translational Data at ELIXIR. She is of the many great speakers at the BioData World Congress in Hinxton, UK that will take place next week (26-27 October 2016). In her presentation during the 2nd day of the Congress, she will talk about maximising opportunities to use human genomics data and about how ELIXIR enables this through European collaborations. Please introduce yourself, your background and your specific role in ELIXIR. Our audience is familiar with ELIXIR already – we interviewed Niklas Blomberg a year ago. I joined the ELIXIR Hub recently as Head of Human Genomics and Translational Data (ELIXIR is the European infrastructure for bioinformatics and life-science data). Prior to joining ELIXIR, I was a Director within the Human Genetics and Computational Biomedicine group at Pfizer. In this role, I led and implemented a genetic and precision medicine strategy to support drug target selection and clinical programmes for the Pain and Sensory Disorders Research Unit. Earlier in my career, I worked within the Toxicogenomics group at GlaxoSmithKline. I gained postdoctoral experience at the University of Cambridge and Imperial College London and a PhD from the University of Cambridge, with a focus […]

DNAdigest interviews The Farr Institute

Interview with Andrew Morris, Professor of Medicine, Director of the Usher Institute of Population Health Sciences and Informatics, Vice Principal of Data Science at the University of Edinburgh and the Director of the Farr Institute in Scotland. Prof Morris will be speaking at the BioData World Congress in Hinxton, UK, 26-27 October 2016. What is The Farr Institute? The Farr Institute is a UK-wide research collaboration involving over 20 universities and health partners in England, Scotland and Wales. The Institute is publically funded by a consortium of ten organisations led by the Medical Research Council. The Institute doesn’t own or control data but analyses data to better understand the health of patients and populations. What kind of research do you support? We are committed to high-quality, cutting-edge research using ‘big data’ to advance the health and care of patients and the public. The Institute works to advance informatics, statistics and data science and to develop governance and infrastructure frameworks that underpin the safe and trusted use of patient data. This provides the necessary tools to investigate, understand and improve the health and care of nation-wide populations. Do you hold any genomic data? The Institute doesn’t hold or own data but […]

DNAdigest interviews DataSHIELD

This interview focuses on the open source DataSHIELD software that enables you to take the analysis to the data, not the data to the analysis. Just like the software itself, this interview is a result of a group effort. D2K group: (from left to right) Dr Andrew Turner, Prof Paul Burton, Dr Demetris Avraam, Dr Stephanie Roberts, Prof Madeleine Murtagh, Dr Olly Butters, Dr Neil Parley, Dr Becca Wilson. The two dogs are the group mascots Java (left) and Data (right). Please introduce yourself. What is your background and your role in the project? The DataSHIELD project is co-ordinated by the Data to Knowledge (D2K) Research Group from the School of Social and Community Medicine, University of Bristol.  The following people are involved in the day-to-day running of the project: Paul Burton – Professor of Infrastructural Epidemiology, Principal Investigator of the overall DataSHIELD project and an active developer of the software and statistical methods. Becca Wilson – originally a planetary scientist – now the DataSHIELD Lead. I coordinate the project and contribute to the expansion of the project beyond biomedical applications. Demetris Avraam – mathematical modeller. I have a leading role in the development, implementation and testing of new statistical […]

Life with an undiagnosed condition: what does it really mean?

The 29th of April is the 4th nationwide annual Undiagnosed Children’s Day. It is organised by SWAN UK (Syndromes Without A Name) – an initiative of the charity Genetic Alliance UK offering support and information to families of children with undiagnosed conditions. Today, we are talking to Claire Walton about what living with an undiagnosed condition means in practice. Claire and Rowan (photo from Claire’s archive). 1)  Could you please introduce yourself and tell us bit about the background? Hi, I am Claire, single mum of 4 children, and we live in Northamptonshire. My daughter is 13, and I have 3 sons aged 10, 8 and 7. All three of my sons have undiagnosed genetic conditions. It is thought that they all have the same ‘thing’ but as yet we do not know what ‘it’ is. They have an array of challenges and issues, including hypoglycaemia, hypothyroidism, possible hypothalamic disorder, growth hormone deficiency, calorie handling issues, GORD, colonic dysmotility, hypermobility with chronic pain, fatigue, hearing issues, developmental delay, speech delay, educational challenges and previous severe failure to thrive, coeliac disease, and other food intolerances. Rowan has an inability to feed ‘normally’, and is therefore reliant on Parenteral Nutrition (Intravenously fed), […]

The culture of scientific research in the UK

The Nuffield Council on Bioethics. Ethics is concerned with what is good and what is bad for individuals and society. Bioethics is a branch of ethics studying the issues arising from the biological and medical sciences. In 1991, the Nuffield Foundation established the Nuffield Council on Bioethics as an independent body that examines and reports on ethical issues in biology and medicine. Since 1994 it has been funded jointly by the Nuffield Foundation, the Wellcome Trust and the Medical Research Council. The Council has achieved an international reputation for advising policy makers and stimulating debate in bioethics. The reports of the Nuffield Council on Bioethics cover multiple topics including public health, research in developing countries, animal research, biofuels, genetically modified crops in developing countries, neonatal medicine, emerging biotechnologies and so on. The main characteristic of these reports is their impartiality: they are based on exhaustive research work conducted under the supervision of independent renowned researchers. An unfortunate fact is that most of these reports are quite lengthy and use “high Academian” – a language not easily understood by people without research experience and scientific background. At DNAdigest we pay close attention to research reports published by the Nuffield Council on Bioethics. Today we present the highlights […]

genetic alliance annual conference. photo of Alistair Kent giving the closing remarks

2014 Genetic Alliance UK Annual Conference

‘Genomic Sequencing; why it is important and how it can help you?’ was no small topic for the 2014 Genetic Alliance UK annual conference. The event called together everyone from researchers to those directly affected by genetic disease. And it was not just the audience that was diverse. With journalist and broadcaster Vivienne Parry, Mark Bale from the Department of Health, and Edward Sherley-Price, the parent of a child recently diagnosed with a genetic disease, all taking to the stage to speak it seemed almost every angle of this debate was covered. So, why is genomic sequencing important? Vivienne Parry, on her whirlwind history of medicine, used the analogy of the Milky Way. Everything is arranged in complex networks and this is why whole genome sequencing is important. From a single lung disease a patient will present completely differently depending on whether they are young or old or overweight, to name just three of the most obvious factors. We cannot isolate and compartmentalise disease as we have tried in the past. Medicine today, unlike in the 15th century (where bloodletting was as high tech as it got), is not limited to treating symptoms. We are increasingly able to deal with […]

Paper money with pound coins stacked on it.

Science Funding: Big Data, Big Spending?

The UK government has committed to spending almost six billion pounds on research infrastructure over the next 5 years. Investments of £1.1 billion per annum from 2016 to 2021 mean the potential to reshape science research infrastructure and secure the future of the UK as a knowledge-based economy. But lets not get too excited just yet. Of course it all depends on how the money is spent. With competing interests and many projects, new and old, vying for a slice of the funds, the billion pound investment can only stretch so far. In recent years prominent scientists have spoken out about (and against) the way science funding is allocated. With media pressure continuing to rise with the increase in online social platforms it seems that the projects that can grab headlines are doomed to be favoured over less ‘glamorous’ options. Yet we have the opportunity to have our own say, to ignore media hype and to comment on what really matters. The Department for Business Innovation and Skills (BIS) has launched a consultation exercise to gather a wide range of views. Science is truly a field that affects us all, however, it is plagued by a lack of public scientific […]

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