collaboration

DNAdigest interviews Pistoia Alliance

Our first interview in 2017 is with John Wise of the Pistoia Alliance. 1) Please introduce yourself, what is your background and your current role? My name is John Wise. I graduated in physiology from the University of Oxford before obtaining a post-graduate certificate in education at the University of London. Nowadays I have a small consultancy practice working in biopharma life science R&D. I spend some of my time working as a business development consultant for the Pistoia Alliance (more about that later) and I also act as the Programme Coordinator for the PRISME Forum which is a not-for-profit, biopharma R&D IT leadership group focussed on the identification and palliation of “hot topics”, and the sharing of industry best practices. I have always worked in life science R&D and in very large part in informatics. I spent the early part of my career in the physiology and then the pharmacology departments in St George’s Hospital Medical School where we had DEC PDP 11s fitted with analogue to digital converters to interface to the experiments. I became very fluent in FORTRAN! Then I joined Sandoz (in the days before it became Novartis) at their Institute for Medical Research located in […]

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 […]

Veterans Affairs Precision Oncology Project

Interview with Louis Fiore, doctor, scientist, manager, innovator at the Department of Veterans Affairs (VA) in Boston Massachusetts, Executive Director of the Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC). Louis will be speaking about the Precision Oncology Project at BioData World Congress USA 2016. 1. Could you please tell us about your background and your role at VA? I’ve been working for VA for almost 36 years. The department of VA takes care of approximately 20 million people, who served in the Armed Forces and are now retired. VA has a network of more than 150 hospitals across the country, they provide all types of healthcare services to veterans. VA has three missions: 1) care for veterans; 2) educate the next generation of healthcare providers; 3) provide research opportunities to improve healthcare of veterans first, and of the greater community as well. The group that I run, MAVERIC, has over 140 employees and works across four divisions: epidemiology and data mining, clinical trials, biobanking, and informatics. We have three national profile projects: Million Veteran Program (MVP), Point of Care Clinical Trial (POCCT) program, and Precision Oncology Program (POP). 2) At BioData World Congress USA 2016 you will be presenting […]

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 […]

DNAdigest interviews Genomic Medicine Alliance – Part 1

As the year goes over, so does our full schedule with interviews. This week, we would like to introduce you to Professor George P. Patrinos. As a member of the Scientific Advisory Committee of the Genomic Medicine Alliance (GMA) he introduced us to the background and workings of the GMA. 1. Could you please give us a short introduction to the Genomic Medicine Alliance (goals, interests, mission)? The Genomic Medicine Alliance (GMA) is a global academic research network. It aims to build and strengthen collaborative ties between academics, researchers, regulators and those members of the general public who are interested in genomic medicine. The GMA focuses particularly on the translation of new research findings into clinical practice in developed, but most importantly, in developing countries. The GMA aims to: Encourage and catalyze multidisciplinary collaborative research between partner institutions and scientists, particularly from developing countries, Liaise between research organizations, clinical entities and regulatory agencies in areas related to genomic medicine, Facilitate the introduction of pharmacogenomics and advanced omics technologies into mainstream clinical practice, Propose guidelines and draw up recommendations in all areas pertaining to genomic medicine, in close collaboration with other scientific academic entities, agencies and regulatory bodies, and, Develop independently and coordinate, in close […]

Centre for Open Science

The Reproducibility Project: Cancer Biology

The Reproducibility Project: Cancer Biology has continued to make steady progress over the last few months.Since December, they have published four new Registered Reports with eLife, and one more has been accepted and on the way.Now that these protocols and analyses plans have been reviewed, the replication experiments themselves can begin. All of the protocols, analyses, and data are freely available on the Open Science Framework (OSF). In total, eleven replications have begun or are poised to begin in the coming weeks.You can keep track of theReproducibility Project progress for all these Registered Reports and all of the rest of the 50 studies included in the project on the Open Science Framework.Take a look at their most recent Science Exchange blog post and read the completed description of their progress so far.

Human Variome Project

Human Variome Project signs MoU with WHO

Earlier this month, Human Variome Project International Ltd signed a formal Memorandum of Understanding with WHO setting out their formal relationship. At the heart of this agreement lays their collaboration in achieving WHO’s goal: to provide the leadership in global health matters that relate to human genomics, with a particular emphasis on service delivery and safety in low- and middle-income countries. The public health implications of advances in human genetics and genomics are of increasing importance to all professionals working in the field. This Memorandum of Understanding gives a new initiative to WHO. While it has always had a small program on genetics and health, focusing mainly on genetic diseases for some time, this new program would  bring a change in focus to the broader issue of human genomics and public health.The Human Variome Project‘s key contribution will be to give a voice to the various health professionals working in human genetics and genomics. The agreement sets out a number of specific areas for collaboration: Creating a co-ordinated international electronic forum to facilitate discussion and interaction between experts, including health professionals, researchers and academics, on matters related to human genomics, global health and service delivery and safety Organizing international meetings on matters related to human genomics and public […]

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 […]

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 […]

DNAdigest interviews Nowomics

This week I would like to introduce you to Richard Smith, founder and software developer of Nowomics. He kindly agreed to answer some questions for our post blog series and here it is – first hand information on Nowomics. Keep reading to find out more about this company.   Richard Smith, founder and software developer of Nowomics 1. Could you please give us a short introduction to Nowomics (goals, interests, mission)? Nowomics is a free website to help life scientists keep up with the latest papers and data relevant to their research. It lets researchers ‘follow’ genes and keywords to build their own news feed of what’s new and popular in their field. The aim is to help scientists discover the most useful information and avoid missing important journal articles, but without spending a lot of their time searching websites. 2. What makes Nowomics unique? Nowomics tracks new papers, but also other sources of curated biological annotation and experimental data. It can tell you if a gene you work on has new annotation added or has been linked to a disease in a recent study. The aim is to build knowledge of these biological relationships into the software to help scientists navigate and discover information, rather than recommending papers […]

DNAdigest interviews SolveBio

DNAdigest continues with the series of interviews. Here we would like to introduce you to Mr Mark Kaganovich, CEO of SolveBio, who agreed on an interview with us. He shared a lot about what SolveBio does and discussed with us the importance of genomic data sharing. Mark Kaganovich, CEO of SolveBio Could you describe what SolveBio does? SolveBio delivers the critical reference data used by hospitals and companies to run genomic applications. These applications use SolveBio’s data to predict the effects of slight DNA variants on a person’s health. SolveBio has designed a secure platform for the robust delivery of complex reference datasets. We make the data easy to access so that our customers can focus on building clinical grade molecular diagnostics applications, faster.   How did you come up with the idea of building a system that integrates genomic reference data into diagnostic and research applications? And what was the crucial moment when you realised the importance of creating it? As a graduate student I spent a lot of time parsing, re-formatting, and integrating data just to answer some basic questions in genomics. At the same time (this was about two years ago) it was becoming clear that genomics was going […]

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 […]

The Duty to Share Patient Information

The duty to share information can be as important as the duty to protect patient confidentiality. Vince Kuraitis and Leslie Kelly Hall released a report discussing in depth topics that concern all of us. They have emphasised and pointed out two things that are missing when talking about data sharing: The explicit recognition of a corollary duty to share patient information with other providers when doing so is the patient’s interest, and a recognition that there is potential tension between the duty to protect patient confidentiality/privacy and the duty to share – with minimal guidance on how to resolve the tension. Their article refers to and discusses three main topics: First of all, Vince and Leslie talk about the recent recognition in the UK, giving us examples from one long-awaited study commissioned by the Department of Health. They have identified the key discoveries from The Information Governance Review Report (Caldicott Review), citing in the essay: …safe and appropriate sharing in the interests of the individual’s direct care should be the rule, not the exception. Caldicott review initial report had suggested 6 acknowledged principles for information sharing, but now the recognition of an explicit duty to share patient information was added […]

hack day

Hack Day August 2014 Summary

This past weekend, our fourth Hack Day brought together some very enthusiastic people along with the DNAdigest team in the Future Business Centre in Cambridge to discuss the development of the Data Discovery Tool we are working on. We are very excited to say that the day turned out to be very productive. Fiona Nielsen, our CEO, started with a short presentation explaining who we are and what we have done so far. Through the course of the day our attendees divided into three groups each discussing different topics while our team integrated a member into each group so that we could follow up with everyone. Interesting discussions on what exactly can be done to improve the existing prototype on data discovery spread around fast and people were really keen on brainstorming new ideas. Hamza, our Nuffield research student, was going around interviewing. He managed to learn about the workflows and the various online repositories used to access genetic data of three Hack Day participants who use human genomic data in their work. The text mining group explored the options for automatically analysing data set descriptions and labelling them with appropriate ontology tags. One very active contributor was Peter Murray-Rust who […]

hack day

DNAdigest Fourth Hack Day

Our Fourth Hack day will be held on the 02/08/14 at 9:30am at the Future Business Centre, King’s Hedges Road, Cambridge, CB4 2HY. Check this map for directions.  The schedule is now available online here. You can also take a look at what we managed to do on our previous Hack Day or explore the storify page of the event. At this the upcoming brainstorm session we will further develop the Data Discovery tools for genomics research using metadata to make data discovery faster, benefiting researchers by accelerating the initial steps of data access.  Join us on the Hack Day by signing up here Hackpad will be our tool of choice for notetaking/collaborating during the day, and we encourage everyone to join with their notes and comments. You are very welcome to tweet and track the progress using our hashtag #DNAhdFor the technically minded, we suggest you bring your laptop. For those more interested in discussions and paper prototyping, just bring your brains and enthusiasm, and we will provide paper materials. There will be lunch and tea/coffee breaks during the day. Don’t Forget to Signup to the event through our eventbrite page on dnadigest4hd.eventbrite.co.uk DNAdigest team is really looking forward to seeing you in Cambridge!

A Scientific Delicacy: Get your own personalised cheddar

Christina Agapakis, a Norwegian biologist at UCLA, has cultured bacteria found in armpits, mouths, belly buttons and toes to make cheese. Its part of a new project, called Selfmade, that came out of Synthetic Aesthetics project whose aim is synthetic biologists, artists and designers from all round the world to collaborate and to investigate what it means to design nature. Agapakis explains that “the dairy on display doesn’t smell or look much different than what you’d find at your local cheese shop” Read more here.  

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