community

A new multi-centralised cryptocurrency: Coinami

Last year we interviewed Can Alkan, an Assistant Professor in the Department of Computer Engineering at the Bilkent University, about Biopeer – a data sharing tool for small- to medium-scale collaborative sequencing efforts. Today we are talking to Can about his new project – Coinami. Please tell us more about Coinami. How did it start? Coinami is basically a volunteer grid computing platform that generates a new multi-centralised cryptocurrency, which uses high throughput sequence (HTS) read mapping as proof-of-work. After Bitcoin gained popularity, many different currencies that are called “altcoins” emerged around the same structure: decentralised, secure transactions in a public ledger called blockchain. All cryptocurrencies basically are composed of two parts: mining, which is generating new coins (i.e. “printing banknotes”), and transactions, which is spending and receiving coins. To provide integrity and prevent “overprinting”, a computationally intensive task has to be performed, which is called proof-of-work. Different cryptocurrency systems use different proof-of-work schemes, but, including Bitcoin, all current proof-of-work tasks serve no practical purpose other than maintaining the currency. Here, we suggest a different approach for proof-of-work. We propose that instead of impractical calculations, the miners should use their computational power for scientific computing. The idea is very similar […]

GenomeConnect: connecting patients and researchers

This is a guest post by the GenomeConnect team. Patients with new genetic diagnoses are increasingly turning to social media and other web resources to try and find other families with the same genetic diagnosis and research opportunities. GenomeConnect, an online patient registry developed as part of the National Institutes of Health funded Clinical Genome Resource (ClinGen) project, is a resource to help patients form connections and partner with researchers to make genomic advances possible. Participation and enrollment in GenomeConnect are open to anyone that has had genetic testing, regardless of diagnosis or test result.  Additionally, participation is completely online allowing individuals from around the world to participate. After completing the online consent process, participants are asked to complete a health survey that reviews each body system to capture basic health information. From there, participants are asked to upload their genetic testing report to allow GenomeConnect staff to capture important genomic information. After participants have shared their genetic and health information through the online portal, that information is prepared for de-identified sharing with approved, publicly available databases, such as NCBI’s ClinVar database, a repository for genomic variants. Once enrolled, GenomeConnect participants have the ability to match with one another via […]

DNAdigest interviews CareAcross

Thanos Kosmidis, a technology and business professional, joined forces with his father, Paris Kosmidis, a medical oncologist with 40 years of clinical experience, to start CareAcross to help patients with cancer and their relatives. What is CareAcross and what is its mission? CareAcross is a digital health company focusing on cancer. Our mission is to support people affected by cancer through credible information, useful tools, psychological support & guidance from experts. Our vision is to facilitate faster, more effective oncology research, and interactions that will improve quality of life of patients and caregivers. We do this through our online platform for patients and caregivers. How and when did it start? What science/research is behind CareAcross? CareAcross.com started in the fall of 2013, when we began putting together a first prototype of an online service for cancer patients and their loved ones. This was after 18 months of research into their “pains, needs and wants”, and the corresponding gaps. Throughout, we have interviewed hundreds of patients and caregivers, and have had roundtables with dozens of healthcare professionals with experience in oncology. These experts continue to be the driving force behind the scientific direction of the company, shaping how we inform, educate and […]

DNAdigest symposium: summary

Last Friday, 21/08, Wayra hosted the DNAdigest symposium “Incentives for data sharing”. On a hot summer Friday in London, we asked the attendees: “How can we create incentives for data sharing in genomics research?” Despite the summer break, we had excellent speakers and a very engaged audience. Both attendees and speakers applauded the great quality of the discussions and the cosy atmosphere of the event. Morning session In the first part, Natalie Banner from the Wellcome Trust, Neil Walker from the University of Cambridge and Shahid Hanif from the Association of the British Pharmaceutical Industry presented multiple prospectives on data sharing. Natalie Banner made it clear that the objective of the Wellcome Trust as a funder is to maximise the benefits for health and society, and gaining the best possible impact of their funding for research. Best possible impact also means maximising data use and utility for reuse, which is why the EAGDA is investigating best practices for data sharing. Natalie’s presentation is available here. Neil Walker presented how funder policies can be difficult to implement for the individual researcher and shared many anecdotes on data sharing and how he uses data management plans to outline for funders how data will […]

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 […]

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 […]

Bringing Genomics to the Clinic: upcoming event of the Cambridge Rare Disease Network

What is a rare disease? Rare (or orphan) diseases are defined as conditions affecting less than 1 in 2,000 people in the EU, or less than 200,000 people in the US, or less than 50,000 people in Japan. In the UK, 1 in 17 people has or will develop a rare disease at some point in their life. There are approximately 6,000 rare diseases identified today and the number is growing. 75% of all rare diseases affect children and 30% of rare disease patients die before the age of 5. 80% of rare diseases are of genetic origin, whilst 20% are the result of infections (bacterial or viral), allergies and environmental causes, or are degenerative and proliferative. Rare diseases are characterised by a broad diversity of disorders and symptoms that vary not only from disease to disease, but also from patient to patient suffering from the same disease. Rare diseases are often chronic and life-threatening and are difficult to diagnose. On average, it takes 6-8 years to diagnose a rare disease. One of the biggest problems is that usually there are no drugs specifically targeting a given rare disease. And since the potential market segment would be quite narrow, pharmaceutical companies are usually […]

Anna Middleton

Involving participants in genomics research

Guest post by Dr Anna Middleton, Senior Staff Scientist, Wellcome Trust Sanger Institute. This blog post was originally published by the Nuffield Council on Bioethics. The blog post is based on the talk Dr Middleton gave at the launch of the Council’s report: The collection, linking and use of data in biomedical research and health care: ethical issues. My career has explored, from multiple different perspectives, the impact of genomics on people. Genomics refers to the study of a person’s 20,000 or so genes. Given the almost infinite ways that people can be genetically different to each other, genomic research often needs to be done on a very large scale in order to be able to interpret the significance of findings, particularly a rare genetic change. So, Big Data and Genomics go hand in hand. To give you an example, I’m currently part of the Deciphering Developmental Disorders (DDD) project at the Sanger Institute which seeks to offer cutting edge genomic testing to 12,000 children from the NHS with severe, complex, physical and/or intellectual disability. These children have exceptionally rare conditions that their doctors may never have seen before. Using an online database that contains large sets of health and biological […]

Data Sharing Game

Research Data Sharing Game

As we all know the reuse of research data definitely benefits the scientific community as a whole, but the decision whether to archive and share these data or not depend primarily on individual researchers. For individuals, it is less obvious that the advantages of sharing data outweigh the associated costs, i.e. time and money. In this sense, the problem of data sharing is like a typical game in interactive decision theory, more commonly known as game theory. By definition, game theory is a study of mathematical models of conflict and cooperation between intelligent rational decision-makers. An obvious assumption herein is that an individual will always try to maximize his or her gains relative to the gains of others. In the paper “A Research Data Sharing Game” Pronk et al create a framework in order to investigate the community gains versus the advantages of the individual researcher in the competitive world of scientific research.  For the analysis, they have designed a simple model of a scientific community where researchers publish a certain amount of papers in a given year and have the choice either to share or not. Via this model, the effect of sharing policies, exploration of several cost scenarios, […]

symposium

DNAdigest Symposium 2014 Summary

This past weekend, DNAdigest organized a Symposium on the topic “Open Science in human genomics research – challenges and inspirations”. The event brought together very interested in the topic and enthusiastic people along with the DNAdigest team. We are very pleased to say that this day turned out to be a success, where both participants and organizers enjoyed the amazing talks of our speaker and the discussion sessions. The day started with a short introduction on the topic by Fiona Nielsen. Then our first speaker, Manuel Corpas was a source of inspiration to all participants, talking us through the process he experienced in order to fully sequence the whole genomes of his family and himself and to share this data widely with the whole world.  Here is a link to the presentation he introduced on the day. The Symposium was organized in the format of Open Space conference, where everybody got to suggest different topics related to Open Science or choose to join one which sounds most interesting. Again, we used HackPad to take notes and interesting thoughts throughout the discussions. You can take a look at it here. We had three more speakers invited to our Symposium: Tim Hubbard (slides) talked about how Genomics […]

symposium

Open Science in human genomics research

UPDATE: only few tickets left – do not forget to register https://dnadigestsym2014.eventbrite.co.uk This November 22nd, DNAdigest is organizing a collaborative symposium. The topic of the event will be “Open Science in human genomics research – challenges and inspirations”. It will take place at the Future Business Centre, Cambridge. You can take a look at this map for directions. At this upcoming collaborative symposium, we will introduce topics like open science, access to sequencing data, privacy concerns around human genomic data, etc., and the schedule of the day will be prepared as a combination of short presentations from invited speakers followed by interactive discussion groups. Join us at the Symposium by signing up here.   You can look forward to inspirational talks to spur excitement and discussions: Manuel Corpas, will talk about how he as a citizen scientist has crowdfunded and crowdsourced the analysis of his personal genome. Linda Briceno, will share her thoughts on legal and ethical implications of data sharing in genomics. Nick Sireau, will talk about how scientists and patients can engage in collaborations, and how Open Science may be either beneficial or challenging in this context. Tim Hubbard, will present how Genomics England is engaging the research community in the 100k […]

data accessibility

DNAdigest published: A Focus on Data Accessibility

The DNAdigest team is very happy to announce that our paper ‘The need to redefine genomic data sharing: A focus on data accessibility‘ has been published in the special issue of the Journal of Applied and Translational Genomics as an open access publication. At DNAdigest, we are aiming to improve the shared amount of genomic data which current state is far from sufficient. Believing is not enough in this case so it was important for us to get some real numbers! We interviewed genetics researchers and ran an online survey in order to find out how much and in what way genomic data is being shared.   Through those in-depth contextual interviews along the online survey, we have managed to assess the state of genomic data sharing. Our finding showed that, although the procedures that researchers follow differ among universities, industry and clinics, there are still many common steps in their workflows. Unsurprisingly, most of the researchers agreed that they do not share enough data and would like this situation to change. If you want to take a look at what else we have discovered, be welcome to read the whole article: T v Schaik et al, The need to […]

dbGaP Improves Access for Individual-Level Genomic Data

“dbGaP Collection: Compilation of Individual-Level Genomic Data for General Research Use” is a new data set collection that is expected to become a very useful tool for researchers. Due to many requests from the scientific community, the NIH brought into play a change in the procedures for accessing aggregate-level data. Most of the dbGaP studies have considerable fraction of participants who consented for “General Research use” (GRU) NIH have recognized and acknowledged those consents to be essentially the same, even though the individuals participated in different studies. As a result this collection was created allowing users to obtain the data. Furthermore, in order to make the process of requesting access less painful and faster, it will be reviewed by a single, central Data Access Committee and users can gain entry through a single access request. The process is identical to those for individual-level, controlled-access data and you can find the instructions for requesters here. Investigators being authorized for access to the datasets within the collection will have the standard one-year approval period. In the meantime, one can choose to use data only from some individuals, but will still have access to all of the information. Additionally, the datasets are going to be updated […]

Genomic Privacy: the Rise of New Research Community

 Genomic Privacy and the Rise of a New Research Community When genomic is mentioned, most people think about huge, heavily-funded international consortia, such as the Human Genome Project. Nowadays, sequencing platforms are readily available meaning that individual labs can actually sequence whole genomes (Whole Genome Sequencing or WGS). For the research in genomics, collecting of a large number of digitalized genomes is of a great importance. As the prices of full sequencing goes down the personalised medicine becomes more and more popular. Of course, the availability of this data will help clinicians run complex tests regarding a patient in a matter of seconds. However, there are issues regarding the privacy due to the unprecedented sensitivity of the genomic data. Lots of funding agencies have now introduced requirements for data sharing while the Personal Genome Project intent to create a dataset of volunteers’ sequenced genomes and make it public for research purposes. However, there are a lot of arguments whether this should be done. Recently Erman Ayday and colleagues created an article stating that the consequences of genomic data disclosure aren’t limited in time and also it reveals a huge amount of information about one’s relatives due to its hereditary nature. This means that […]

We’ve been answering questions on reddit!

We love talking to you all. So much so we’ve been talking to the different scientific communities and as such Check us out doing AMA’s on reddit: Genetics: http://www.reddit.com/r/genetics/ Bioinformatics: http://www.reddit.com/r/bioinformatics/ Genomics: http://www.reddit.com/r/genomics/ Science: http://www.reddit.com/r/science/ Any questions we have not answered yet? Drop us a line 🙂 Science: http://www.reddit.com/r/science/

£8 million raised will help save lives

Viral Selfie Raises £8 million for Cancer Research

Incredibly, over £8 million has been raised for Cancer Research in just 6 days after the ‘no-make-up-selfie’ went viral. It is an amazing example of the power of sharing and highlights how much of a difference can be made when the public are empowered. These are ideals that need to be incorporated more thoroughly into the scientific research itself – not just the funding for the research. If you have somehow missed out on the trend it is an incredibly simple and effective process whereby individuals post a photo of their make-up-less face, a screenshot of their text donating £3 to charity, and publicly nominate a few selected friends to do the same. It follows the same format as a number of other recent viral campaigns, perhaps most (in)famously ‘neknominations’ a craze which swept the Facebook newsfeeds of university students everywhere. I think we can all agree that the viral selfie is just a tad more worthwhile. Despite the enormous sums of money raised by the viral campaign it is not without criticism. Arguably it is a great shame that in todays society it is viewed as brave for a woman to reveal her make-up-less face. This is a sight which […]

Thunderclap: Lend Us Your Social Media Voice

We are excited to announce that we have now launched our Thunderclap. We would love for you to lend us your social media voice to help spread the word about the importance of data sharing in genetics and the work of the DNAdigest charity. Joining up takes just seconds and could have a massive impact. By joining you allow a one-off message to be automatically shared to any of the social media accounts which you have chosen to link. By signing up to our Thunderclap campaign you can help to strengthen the DNA Digest voice and make sure as many people as possible are aware of the importance of data sharing in genetics and of the challenges and solutions that surround this topic. We greatly appreciate your support!

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