Fiona Nielsen

The Patient Group Handbook – now in print!

Great news for rare disease patient groups announced by Nick Sireau and Findacure:  Dear friends, We’re very pleased to say that our latest book – The Patient Group Handbook: A Practical Guide for Research and Drug Development – is now available both in print and ebook formats on Amazon: On Amazon.co.uk in print On Amazon.com in print Or as an ebook All royalties are donated to Findacure, the charity we set up to help rare disease patient groups. Please buy the book and spread the word among your networks. Thank you! Nick and Tony Co-founders, Findacure About the The Patient Group Handbook: This new book edited by rare disease experts Anthony Hall and Nicolas Sireau provides a collection of chapters by world leaders in the field of orphan diseases and drugs in order to help patient groups grow fast and sustainably. As a practical, hands-on guide for research and drug development, it provides tools and advice on topics such as: – How to set up and manage a patient group: US and UK perspectives. – How to build an international research consortium. – How to promote basic research. – How to engage with academia for drug discovery. – How to engage with industry. […]

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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 […]

YAAC conference

YAAC – Leveraging Open Science to facilitate interdisciplinary cancer research

The Young Alliance Against Cancer (YAAC) held its second conference on May 22-23 in Copenhagen. Fiona Nielsen attended the conference and had the organisers Benito Campos and Lars Rønn Olsen answer some of her questions. Fiona: The Young Alliance is lead by a group of young cancer researchers, but how and why did the Young Alliance start? Benito: It all started out in 2011 when a group of us (Aaron, Lars, Kunal, Benito) realised that cancer research is so complex and a large challenge for young researchers, and the narrow focus of each researcher brings a risk of doing redundant work because you are missing developments in the field. For instance we saw that publicly available data and tools from our lab could easily be unknown by the researchers in the next lab. We decided that it is necessary to help the young researchers know what data and tools are available. For just a small effort on increasing knowledge sharing, we could see a potential for making a big impact. We also saw the need for interdisciplinary knowledge exchange, so we decided to create an organisation to bring together young scientists with diverse backgrounds but with a common interest in […]

DNAdigest partners with KPMG

The global consultancy firm provides DNAdigest with expert support KPMG, a leading consulting firm in security audits is partnering with DNAdigest. In December we signed our partnership agreement with KPMG in which DNAdigest will receive pro-bono support towards designing our secure platform. Thanks to the social commitment of KPMG, DNAdigest will benefit from expert advice to implement security by design. The partnership agreement includes feedback on our platform design as well as active engagement in our workshops and hackday activities. Stay tuned to our newsletter for announcement of our upcoming events! 

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Pharmacology Matters present DNAdigest

The December issue of Pharmacology Matters is focused on personalized medicine    In an invited contribution, Fiona Nielsen from DNAdigest is commenting on personalized medicine in the latest issue of Pharmacology Matters. You may read the online version of the December issue here: Pharmacology Matters – Brave New World? The opportunities and challenges of personalized medicines.

Would you share your genome? Meetup in Cambridge

Open Research Meetup in Cambridge – Lively discussion followed the intro videos and presentation On December 16th Fiona Nielsen gave a presentation at the Open Research meetup in Cambridge. The meetup organiser had invited DNAdigest to participate in a discussion on genomics and data sharing. Keren asked the question “Would you share your genome?” and introduced the evening with a video explaining what a genome is and what it means to have your genome sequenced. Fiona gave a presentation on the field of genetics data sharing including topics such as data sharing for research, patient consent and direct-to-consumer genetic testing. The audience was an approximately 50/50 division of researchers vs other professions which gave an insightful discussion on the advantages of genetic research and the potential risks of data sharing and the high hopes of the impact of genetics on the future of medicine.  The slide presentation can be downloaded from SlideShare. The Open Research meetup is a chapter initiated by members of the Open Knowledge Foundation. You can read about their upcoming events on their OKFN web page: http://science.okfn.org/community/local-groups/cambridge-open-research/

Would you share your genome?

DNAdigest in Cambridge for the Open Research meetup The new Open Research meetup group in Cambridge has invited DNAdigest to participate in a discussion on genomics and data sharing. The event on December 16th at the Panton Arms  is titled ‘Would you share your genome?’ We will be discussing what are the options today for data sharing and what do they entail in terms of privacy, benefit for research, and personal risks. Read more and sign up for the event through eventbrite: http://www.eventbrite.co.uk/e/would-you-share-your-genome-sequence-tickets-9293969513  

WISE awards

WiSE award winners + photos

WiSE awards winners + photos Congratulations to Julie Barnes the winner of the WiSE award for Entrepreneurship and Innovation 2013. If you do not know of Julie Barnes already, please take the time to look up the great work she is doing as CEO of Abcodia. For the rest of the award winners, have a look at the WiSE campaign website: WiSE award winners 2013 And browse through the pictures from the day at SaturEyes.com.

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Anonymization and patient consent discussed at PACCR

On her blog Kerstin Forsberg reports on the many opinions expressed relating to de-identification (anonymization) and patient consent for data sharing. One patient advocate at the conference stated “No-one ever asks if you want to be de-identified or not”.   For the individuals who do not mind all their data to be entirely public (i.e. not fully de-identified) projects like the Personal Genomes Project is an option to contribute all your genomic data and medical data for open access and public use without any promises of privacy. Since last week the Personal Genomes project launched in the UK, and they have put a call out for 100,000 volunteers to donate their data: personalgenomes.org.uk The options today are all-or-nothing both with respect to anonymization and data sharing. We want to provide an alternative to meet the needs of both patients and researchers: DNAdigest is developing a platform to apply a patented mechanism for data sharing allowing variable levels of anonymization. Our mission is to enable the widest possible reuse of genomic data within the consent given by the individual donating the data. 

open-steps

Open-Steps interview Fiona Nielsen, CEO of DNAdigest

Open-Steps is discovering and showcasing Open Knowledge projects around the world Since July 2013 Marguerite and Alejandro have made an incredible journey through Europe, Turkey and India to discover and describe the Open Knowledge projects they find on their way. And they are not done yet! Next Margo and Alex will visit South-East Asia, Japan and South America. You can follow their travels and their stories on Open-Steps.org. As one example of an Open Knowledge project in Europe, Margo and Alex have interviewed Fiona Nielsen about the DNAdigest initiative to open and broaden access to knowledge in the context of human genomics data. Read the interview here: Interview with Fiona Nielsen, CEO DNAdigest.org, Cambridge UK

hackday

DNAdigest hack day on privacy and security

Hack day in London on November 23rd DNAdigest coordially invites you to our upcoming Hack Day in London on November 23rd. The schedule and details of the day are being filled in now on our new DNAdigest tumblr site and registration is now open through Eventbrite. The topic of the day is privacy and security issues related to genomics data sharing. We will also welcome related discussions on metadata, data indexing, query interface, data exchange protocols, etc. Keep an eye on our tumblr page for more background info as it becomes available. If you have any questions, do not hesitate to get in touch on info@dnadigest.org Looking forward to see you in November!

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DNAdigest press coverage and Nick Clegg visit

One day ahead of the official opening of Wayra UnLtd academy – we are in the news!   The official opening of the Wayra UnLtd academy happened this Monday, with big press coverage and a visit from the UK deputy prime minister Nick Clegg. Read the article at the Sunday Times: ‘Wikipedia of genes’ to help fight disease’ And the summary of Nick Cleggs visit in Business Matters: ‘Deputy PM Nick Clegg opens social enterprise accelerator Wayra UnLtd’ Photo courtesy: Business Matters

2013 WiSE awards

Fiona Nielsen shortlisted for WiSE awards 2013

Join us for the award ceremony on November 14th  The association for Women in Science and Engineering have announced their shortlist of nominees for the WiSE awards 2013. We are proud to highlight that Fiona Nielsen, CEO of DNAdigest, has been shortlisted in the category Enterprise and Innovation. The award ceremony will take place in the Science Museum in London on November 14th and tickets are still available. Join us to celebrate women who make their mark in science and technology.Tickets are selling out, so secure your seat now by contacting Rebecca Winstanley r.winstanley@wisecampaign.org.uk

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Nuffield reports on privacy and data control

The Nuffield Council on Bioethics held their second fact-finding meeting on September 12th. The summary from their latest meeting presents the combined expert knowledge of the current status of patient privacy in relation to data access issues in research and clinical practice. Some interesting points were raised during the meeting, including: patients do not necessarily value privacy to the exclusion of all other interests; the engineering techniques for providing complex data controls to patients and participants exist, but the political will to implement them is often lacking; Read the whole list and summary on the councils webpage, and sign up to their newsletter to stay up-to-date with their work on biomedical and health data.

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Data sharing for cancer in the cloud

The latest example of how collaborative data sharing enables new discoveries. The Cancer Genome Atlas (TCGA) Pan-Cancer project involved more than 250 collaborators from 30 different institutions who collected a common standardised dataset of 12 types of cancer assayed for both genomic and epigenomic features. The dataset was shared with the entire pan-cancer project through the cloud platform Synapse which provided a collaborative environment for data analysis. The effort resulted in four Open Access papers published in Nature Genetics, and the collaboration is summarised in this editorial: http://www.nature.com/ng/journal/v45/n10/full/ng.2780.html

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Research Data Alliance 2nd plenary

If you missed the second plenary meeting of the Research Data Alliance which was held in Washington DC, you will be delighted to know that the live webcasts were recorded and available via TVworldwide: Webcast recordings for the RDA plenary meeting in Washington September 16-18, 2013 You may also like to review the state of the Research Data Alliance in facts and figures as presented by Mark A. Parsons demonstrating a growing interest in data sharing and related topics in the research community. State of the Research Data Alliance by Mark A. Parsons

DNAdigest Hack Day

DNAdigest workshop at ICSB2013

On August 29th DNAdigest organized a pre-conference workshop for the ICSB conference. Our workshop was titled “DNAdigest: translational genomics – from bioinformatics to medical informatics”. Our international audience were treated with three invited talks and a presentation from DNAdigest. The three invited talks covered the whole spectrum of translational genomics from mining medical records for disease associations, to technology and methods, to analysis of individual genes in individual patients to identify disease-causing mutations. Ben Curran (@3rdKingsland) attended our workshop and wrote no less than two summaries on his blog: The talk of Søren Brunak: Adventures in Daneland The rest of the talks: While its fresh-ish And you can download the DNAdigest presentation here: Workshop ICSB August 29 2013 – DNAdigest (PDF) The schedule was: •9:00am Introduction •Søren Brunak, Professor, Center for Biological Sequence Analysis: Data mining medical records for new insights for diagnostics •Q&A •Jennifer Becq, Bioinformatics Scientist, illumina Cambridge: From sequencing a tumour sample to finding actionable variants •Q&A •Mette Nyegaard, Associate Professor Human Genetics, Aarhus University: A novel deafness locus and gene mutation on chromosome 6q15-q21 identified using linkage analysis and next generation sequencing •Q&A •Fiona Nielsen, DNAdigest.org: Protecting data and sharing knowledge – Enabling secure data access for advancement of […]

Mike Galsworthy speaking

How to recognise a shrew… and Open Data

Excellent poetry/science mix by Mike Galsworthy The Open Science and Open Data proponent Mike Galsworthy also happens to be an excellent poet. For your afternoon entertainment, we recommend watching this 10 min YouTube clip from the Science ShowOff of July 17th. Mike presents first his personal ode to David Attenborough in form of a poem about how to recognise a shrew… and then he gives his 2 cents on Open Data. Enjoy! 🙂 If you want to hear more from Mike Galsworthy on Open Data, have a look at his recent article: “Funding bodies will have to force scientists to share data“.

Fiona Nielsen

DNAdigest gave live pitch at Nerve conference for disruptive technologies

Last week, as part of the Kickstart challenge for the Nerve conference for disruptive technologies, DNAdigest was presented on stage by Fiona Nielsen. The conference program included high-profile speakers from Google and NASA as well as less known inventors and entrepreneurs presenting their disruptive technologies from brain imaging to airborne motorcycles. It was a tremendous inspiring event. Thanks to all who supported us in the Kickstart challenge competition!

Global Alliance for data sharing in genomics

These are exciting times for genomics research! Last week  more than sixty organisations around the world announced the formation of a global consortia, the Global Alliance, to enable data sharing in genomics research. The intention of this consortia is to develop standards, similar to how W3C developed standards for the internet, so that the research data around the world will have common representation formats and become interoperable. The more institutions sign up for a common public position on the necessity of standards and data sharing to advance scientific research the better. But the work is not done by developing standards alone. The implementation of these standards over institutions that traditionally have used multiple and ad-hoc solutions for data storage and management is likely to take a while. In the meantime, there is a need to develop tools and mechanisms for interacting with and exchanging data to support the emerging standards, and this is the focus of DNAdigest. DNAdigest is developing a platform for accessing genomics data across institutions, opening up access, creating value for research, while maintaining data privacy. We work with the existing and developing standards and fully support the Global Alliance initiative and the development of open technology standards. […]

RDA Third Plenary Session

Data publication working group – A new initiative by Research Data Alliance

At the launch of the Research Data Alliance, an Interest Group on Publishing Data was initiated, building on the existing framework of the ICSU-WDS Data Publication Working Group. ICSU-WDS existing subgroups will seek RDA Working Group endorsment and other Working Groups may be created under the umbrella of the RDA/WDS Interest Group on Publishing Data. Fiona Nielsen from DNAdigest is participating in the Bibliometrics subgroup to develop recommendations for data publishers and science publishers to further the development of best practices for data accessibility and reuse.

BOSC 2013: Bioinformatics Open Source Conference, July 19-20

DNAdigest will be presenting a talk and a poster at the Bioinformatics Open Source Conference. The BOSC will take place in Berlin in conjunction with the annual ISMB/ECCB conference. You can register for the event through the conference registration for ISMB/ECCB 2013. We are participating in the session on Open Science and Reproducible Research: “Open Science and Reproducible Research — New this year, this session encompasses the theory and practice of open science, including open notebook science, open data, transparent and reproducible workflows, and shared standards for reviewing and publishing research papers.“ The BOSC keynote speakers this year will be Sean Eddy of the Howard Hughes Medical Institute’s Janelia Farm and Cameron Neylon from Public Library of Science (PLoS). It is promising to be a great event, so come join us in Berlin.

Workshop: Translational Genomics at ICSB13

DNAdigest will be organising a workshop entitled  “Translational genomics – from bioinformatics to medical informatics” at the International Conference on Systems Biology 2013 in Copenhagen. The workshop will be held on Thursday August 29th at DTU, Lyngby. In this workshop we will present the current challenges in translational genomics. We will discuss how research findings in genomics can be linked to and have an impact for medical diagnostics. Four presentations will cover the views from bioinformatics to medical genetics. There will be time set aside for Q&A with our presenters, and we will encourage you to participate in the discussion. Søren Brunak, Professor, Center for Biological Sequence Analysis: Data mining medical records for new insights for diagnostics Jennifer Becq, Bioinformatics Scientist, illumina Cambridge: From sequencing a tumour sample to finding actionable variants Mette Nyegaard, Associate Professor Human Genetics, Aarhus University: A novel deafness locus and gene mutation on chromosome 6q15-q21 identified using linkage analysis and next generation sequencing Fiona Nielsen, DNAdigest.org: Protecting data and sharing knowledge – Enabling secure data access for advancement of genomics research See the complete workshop program on the ICSB13 homepage. And register for the workshop along with your conference registration. Looking forward to seeing you in Copenhagen! — […]

dna digest logo

W3C workshop: Open Data on the Web, April 23-24 2013 #ODW13

On April 24th we presented the DNAdigest initiative for an international assembly of Open Data pioneers from government, industry and academia at Google Campus in London. You can read the abstract on the ODW13 homepage, and download the presentation as PDF: W3C Open data on the web April 24 2013 – DNAdigest. Thanks to the W3C, the Open Data Institute and the Open Knowledge Foundation, the current players in the field were given an excellent opportunity to exchange experience and know-how, both on implementation and adaptation of Open Data standards. Read more on twitter using the hashtag #ODW13. Tweets about “#odw13” //

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