data

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 […]

The key elements of good data sharing practice

This is a guest post by Wellcome Trust. Originally published on blog.wellcome.ac.uk The Wellcome Trust is a leading partner in the Public Health Research Data Forum, which brings together research funders who are committed to increasing the sharing of health research data in ways that are equitable, ethical and efficient and will accelerate improvements in public health. On behalf of the Forum, the Trust funded a major international study of stakeholders’ views about best practices for sharing public health research data from low and middle income settings, which recently published its results. Dr Susan Bull and Prof Michael Parker, from The Ethox Centre, University of Oxford, discuss the key issues and findings of the study. Data-sharing is increasingly seen as an important component of effective and efficient biomedical research – both by researchers, and research funders. At the same time, it is recognised that efforts to increase access to individual-level data raise important ethical and governance challenges, some of which may vary depending on the context in which the research takes place. The primary argument in favour of more routine sharing of de-identified research data is its potential to generate more – and higher quality – science. This could in turn lead to improved health outcomes, and promoting […]

OpenTrials

Open Knowledge announce plans for OpenTrials

OpenTrials will collect information about all clinical trials around the world Before any drug goes on the market, it usually takes several years of clinical trials to make sure that the drug is safe to use and is effective against the disease. In reality, some drugs are better than others and many drugs have severe side effects in particular groups of patients. Patients, doctors, researchers and policy makers often rely on the results of clinical trials to make informed decisions about which drugs are best. For multiple reasons, only about half of all clinical trial results are published. Positive results are published twice as often as negative results. And very often not all important details about the methods and findings are published. It is therefore exciting news that Open Knowledge announced the development of OpenTrials – an open, online database of information about the world’s clinical research trials. Open Trials will collect information from different existing sources and provide a clear picture of the data and documents on all trials conducted on medicines and other treatments around the world. The project is designed to increase transparency and improve access to research. It will be directed by Dr. Ben Goldacre (@bengoldacre), an internationally known leader on clinical transparency. You can take a look at his […]

Code for Genomic and Health-Related Data Sharing

The sharing of scientific, genomic and health-related data for the sake of research is of a fundamental importance in order to provide continuous progress in our understanding of human health and wellbeing. While collaboration for data sharing is increasingly embraced by policymakers and the international biomedical community, we still lack a common ethical and legal framework to connect regulators, funders, consortia, and research projects to facilitate genomic and clinical data linkage, global science collaboration, and responsible research conduct. Such framework will definitely assist in the progress of global science and responsible research conduct. This is why BioSHaRE researchers in collaboration with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations started to work on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. This international code will give us the guidance on how to responsibly share genomic and health-related data. It also pushes for better access to the shared data, knowledge, and resources in presently under-served regions. Discussions on the topic had started back in 2013 and are currently continuing. The Code is built around a set of foundational principles and guidelines. It: interprets the right […]

research data

Giving research data the credit it’s due

Guest post by Sarah H Carl (@sarahhcarl) In many ways, the currency of the scientific world is publications. Published articles are seen as proof – often by colleagues and future employers – of the quality, relevance and impact of a researcher’s work. Scientists read papers to familiarize themselves with new results and techniques, and then they cite those papers in their own publications, increasing the recognition and spread of the most useful articles. However, while there is undoubtedly a role for publishing a nicely-packaged, (hopefully) well-written interpretation of one’s work, are publications really the most valuable product that we as scientists have to offer one another? As biology moves more and more towards large-scale, high-throughput techniques – think all of the ‘omics – an increasingly large proportion of researchers’ time and effort is spent generating, processing and analyzing datasets. In genomics, large sequencing consortia like the Human Genome Project or ENCODE  were funded in part to generate public resources that could serve as roadmaps to guide future scientists. However, in smaller labs, all too often after a particular set of questions is answered, large datasets end up languishing on a dusty server somewhere. Even for projects whose express purpose is […]

DNAdigest interviews NGS logistics

NGS logistics is the next project featured in our blog interviews. We have interviewed Amin Ardeshirdavani who is a PhD student involved in the creation of this web-based application. Take a look at the interview to find why this tool has become very popular within KU Leuven. Amin Ardeshirdavani 1. What is NGS logistics? NGS-Logistics is a web-based application, which accelerates the federated analysis of Next Generation Sequencing data across different centres. NGS-Logistics acts as a real logistics company: you order something from the Internet; the owner processes your request and then ships it through a safe and trustful logistics company. In this of NGS-Logistics, the goods are human sequence data and researchers ask for possible variations and their frequency among the whole population. We try to deliver the answers in the fastest and safest possible way. 2. What is your part in NGS logistics? Right now I am a PhD student at KU Leuven and the whole idea of my PhD project is designing and developing new data structures for analysing of massive amount of data produced by Next Generation Sequencing machines. NGS logistics is exactly that. I have done the whole design and development of the application and database. Hereby I […]

DNAdigest interviews Aridhia

As promised last week in the DNAdigest’s newsletter, we are giving life to our first blog post interview. Be introduced to Mr Rodrigo Barnes, part of the Aridia team. He kindly agreed to answer our questions about Aridhia and their views on genomic data sharing.  Mr Rodrigo Barnes, CTO of Aridhia 1. You are a part of the Aridhia team. Please, tell us what the goals and the interests of the company are? Aridhia started with the objective of using health informatics and analytics to improve efficiency and service delivery for healthcare providers, support the management of chronic disease and personalised medicine, and ultimately improve patient outcomes. Good outcomes had already started to emerge in diabetes and other chronic diseases, through some of the work undertaken by the NHS in Scotland and led by one of our founders, Professor Andrew Morris. This included providing clinicians and patients with access to up-to-date, rich information from different parts of the health system. Aridhia has since developed new products and services to solve informatics challenges in the clinical and operational aspects of health. As a commercial organisation, we have worked on these opportunities in collaboration with healthcare providers, universities, innovation centres and other […]

Participants looking at some of the brainstorm post-it notes

OKFN workshop: Open Data, Personal Data and Privacy

This week the Open Knowledge Foundation ran a workshop on Open Data, Personal Data and Privacy. A recurring theme of the OKFN workshop was the interface of personal data and OpenData. The benefits of making data as easily available as possible are vast but it comes with a very sensitive issue attached. Protecting the privacy of individuals is paramount. The advantages of the transparency that OpenData brings are obvious, but for which purposes is it relevant to include personally identifiable information (PII) as OpenData, and to what extent is it possible to transform PII to OpenData or Open Knowledge. When it comes to Open Data, personal data and privacy it is important to tread carefully. One strong message from the workshop was the complexity of communicating both OpenData and privacy. For each of these terms the participants brainstormed their associations and found that the connotations of these terms vary widely depending on your background and the context the terms are applied in.  Our CEO Fiona Nielsen participated in the OKFN workshop and chaired a discussion session on the topic of data transformation through aggregation and to what extent this can be applied to transform data to openly available data sets or OpenKnowledge. If you […]

The DNA Digest Write for Data Sharing competition.

The DNAdigest Write For Data Sharing Essay Competition

We are pleased to launch our first essay competition, we are looking for entries of 800 words in answer to one of our questions in the theme of data sharing in research. The winner will receive a £200 cash prize and finalists will have their work published on the DNA digest website, as well as honourable mentions. Please choose from one of these questions more information and helpful tips for the questions are on the essay competition page. 1) What is the current state of data sharing in 2014 and how can we encourage best practices for ethical and efficient data sharing? 2) Describe a time in your research when data sharing had a positive impact or when lack of data sharing had a negative impact on your research. 3) Describe a time when data sharing has had a negative impact on your research? 4) How do you imagine the future of data sharing in healthcare or research? The judging panel includes Dr Adam Harman-Clarke from Geneix, Dauda Bappa Project Manager from StoreGene and Amy Marquis curator at the Fitzwilliam Who will be looking for articles with the best written style, insight of content and the societal relevance of the writing. Prize: £200 Entries […]

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