science

A better cancer treatment for children: we can create it together!

Children with cancer often don’t have access to innovative drugs in the way adult patients do. Why? Today we talk to Cesare Spadoni, founder of the aPODD foundation (Accelerating Paediatric Oncology Drug Development), about the current situation with childhood cancer and how it can be changed. 1. What is your background and how did you get involved with the project? I am a scientist and a drug development professional that has been working in business development roles for the past 12 years. But I am also a parent that one day heard the most terrifying words any parent may hear. My daughter was diagnosed with cancer at the age of three. After a year-long struggle with the disease she passed away in my arms. This was the time I resolved to do something for children with cancer. 2. What is the aim of your project and how did it start? The major problem facing children with aggressive forms of cancer is the lack of access to innovative treatment options. Children with cancer are generally treated with radiotherapy and old cytotoxic drugs that were approved 40-50 years ago in some cases. Sick children do not have access to the most innovative […]

ecology concept

Ecological Perspective on Data Sharing

We have invited Charlie Outhwaite (@charlielouo) to write a guest blog post on the topic of openness and data sharing from an ecological point of view. The post give us the great opportunity to draw a parallel on how the same type of data sharing problems we are experiencing in the field of genomics are observed across different scientific disciplines. The field of ecology is a vast and varied one. As a result, the types and quantities of data produced differ hugely.  Whether a study is small in scale, such as a field or lab based project, or a large, country or global scale, big data study: the amount of data that could be made available is enormous.  Yet the field of ecology has been considered as behind in terms of its openness when compared to other areas of biology such as genomics. With such vast amounts and types of data available, sharing that data openly has the potential to boost research opportunities and open up collaboration within and between fields. As is the case within many scientific disciplines, a major barrier for data sharing in ecology is the fear of being scooped. For this reason, many researchers would be unlikely […]

DNAdigest interviews Transcriptomine

This week I would like to introduce you to Dr Neil McKenna who is a principal investigator of the Nuclear Receptor Signaling Atlas consortium. In the following A&Q session you will learn about the tool Transcriptomine which gives the research community ready access to transcriptomic datasets – some background, future plans for improvement as well as step-by-step process for you to start using it for your research. Dr Neil McKenna, principal investigator of the Nuclear Receptor Signaling Atlas consortium 1. Could you please give us an introduction to Transcriptomine? Eukaryotic signal transduction involves small extracellular signaling molecules (ESMs) – hormones and growth factors, for example – and transcription factors (TFs), which bind DNA and regulate the expression of target genes. Transcriptomine is an effort to compile, organize and consistently annotate transcriptomic datasets involving ESMs or TFs, and to expose these to the research community so that they can make more effective use of them for their research. 2. What is your role in the project and how does you background support it? Transcriptomine draws together the talents of a scientific curation and annotation team, with a strong background in signal transduction research, and a web development and information technology team. Financial support for Transcriptomine is […]

viral metagenomics

Viral Metagenomics in the Field and in the Clinic

I am very happy to present you a summary of the paper “Beyond research: a primer for considerations on using viral metagenomics in the field and clinic” to which our CEO, Fiona Nielsen, is a co-author. The paper by Hall et al discusses the issues arising when considering metagenomics sequencing for critical applications in the field or clinical applications. What is metagenomics? Usually researchers obtain genetic material (e.g. DNA) from a single source – from an individual patient, isolated plant, fungus, bacteria, virus, etc. But in reality, there are many situations in which myriads of different organisms are present together and it is impossible to isolate their DNA individually. Examples include plants, fungi, and bacteria living in soil or water in a certain area, gut flora living in the human digestive tract, different viruses that affect animals and plants etc. Metagenomics studies genetic material obtained directly from environmental samples, allowing one to identify all species present in the sample at once. This makes metagenomics a very powerful diagnostic tool, and clinical laboratories are about to start using it. But before it takes off, there are several serious issues that need to be sorted out. Hall and collaborators highlight some of […]

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.

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, […]

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 […]

NIH Policies Improving Data Sharing

Policies put into place by major funding agencies like the National Institutes of Health (NIH), and to a lesser extent by scientific journals, aim to increase the sharing of scientific resources among life science investigators. There have been a lot of changes in data-sharing policies over the past 10 to 12 years, and new tools for data-sharing have become available. says lead author Genevieve Pham-Kanter , PhD, assistant professor of Health Management and Policy at Drexel University School of Public Health. He also adds: At the same time, there have been moves by many universities and academic health centers to preserve their intellectual property and limit sharing. Since there had been very little systemic evaluation of how these policies have affected scientists and their sharing behavior, we wanted to get a sense of which policies were working and which were not. In order to measure the influence of those policies, Pham-Kanter and her co-authors – Eric G. Campbell, PhD, Mongan Institute for Health Policy at MGH, and Darren Zinner, PhD, Heller School for Social Policy and Management, Brandeis University – launched a survey. Almost 1,000 out of 3,000 investigators completed and returned this survey. 65 percent of them believed that NIH […]

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 […]

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 […]

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 […]

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.  

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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