Posts tagged: open science

Why we need badges in science


In the world of research, as with most vocational settings, there’s a lot that gets done that goes unrecognized. That unrecognized work can not only be crucial for getting to the actual research outcome put forward in the form of publications, but also for reflecting important skills gained.

Yet, outside of the traditional means of credit—such as degrees, publications, role titles—there is no real way of recognizing this skill with the same issuing authority as with which one receives a degree or publication. The idea that these skills deserve recognition is gaining ground.

Recently, the Wellcome Trust, MIT, Digital Science, and others have come together to create a taxonomy of contributorship. It recognizes roles like data curation, development of design methodology, …

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MozFest: Bringing the Web to Science


In just a month’s time from now, Mozilla will be hosting their annual Mozilla Festival (“MozFest” for short), which for the 2nd year will feature a Science Track, which this year we will be contributing to through a 3-hour sprint on author contributorship, the journal article, and the Open Badges Infrastructure. We’re organising this with our friends at PLoS, the Wellcome Trust, ORCiD, Digital Science, and Digital Me. Look out for our blog in the next few days where we’ll go into more detail about this session.

MozFest is where communities working in technology, design, education, journalism, and research come together to innovate in the space of the Web. It’s for coders and non-coders alike. Bring everything …

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Keeping up with the Jobses: the role of technology in reproducible research

Group photo (click for full picture)

AllBio's workshop on 'reproducibility in research' saw a metaphorical bottle smashed against the bow of The Genome Analysis Centre (TGAC)'s shiny new training facility.

Fueled by hackpads, marker pens and a mountain of tea and biscuits, the workshop (a mixture of research scientists, PhD students, coders, funders and publishers) set about asking the question: 'what are the barriers to reproducible research?'

Group photo (click to enlarge)

Running to stand still

AllBio was established to bring the technology of bioinformatics to a diverse set of biological disciplines, but with this workshop it stepped across to research's flipside: publishing.

Whether data or papers, it is clear that advances in technology have much to offer when it comes to improving …

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Together we are stronger: charities join forces to support open access


A consortium of six leading UK medical research charities will support the costs of making research articles from their funded research immediately and freely openly available to scientists, patients, and donors alike, through the recently announced joint Charity Open Access Fund. David Carr of the Wellcome Trust, Sanjay Thakrar of the British Heart Foundation and Matt Kaiser of Leukaemia & Lymphoma Research explain how this new partnership came about.

As charitable funders of medical research, we are dedicated to maximizing the societal benefits that flow from the research we fund. We know that making research publications openly available ensures that the knowledge and data they contain can be more widely accessed, corroborated and used to advance research …

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‘You might as well patent oxygen’ – an unashamedly unbalanced take on Australia’s support for gene patents

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Last year, a rainbow coalition of civil liberties campaigners, cancer patients and eminent geneticists – heck, even Jim Watson! – argued before the US Supreme Court that gene sequences are a product of nature and therefore ineligible for patent protection.

And the Supreme Court replied, in all its refined wisdom:

'Well, duh!'

A nine-to-nothing unanimous decision.

A difference of opinion

But the US has long known that truths held to be 'self-evident' are not always in for a smooth ride, and so we perhaps should not be too surprised – if still perplexed and saddened – to learn that the Australian Federal Court, when faced with the same question, responded: 'um, maybe not'.

I do not pretend to understand what brand of logic could …

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Announcing the Great Galaxy GigaScience (G3) Open Science Workshop

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This is a guest post by Dr Nick Wong, a researcher in developmental epigenetics at The Royal Children’s Hospital in Victoria, Australia. Dr Wong is taking part in the G3 workshop. Register for free here.


Having been quite versed in the art of research 8 years post PhD, I have been very fortunate to witness a renaissance in publishing in two ways. First, I remember quite well during my PhD training (over 10 years ago), the process of preparing a manuscript for the highest ranked journal—submit, reject, reformat and submit to the next journal, reject, submit . . . you get the story. During that time, Impact Factor was the key metric in which a journal was measured. This evolved quickly …

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Making predictions: The future of biology


It’s hard to make predictions, especially about the Future.

Yogi Berra (via Titus Brown)


What will biology look like in the year 2039? In July I attended the Bioinformatics Open Source Conference (BOSC), a friendly community of open source advocates, where I heard bioinformatician Titus Brown deliver his thoughts on this in his talk, “A History of Bioinformatics (in the Year 2039)”.

Good for my jet lag and a great start to BOSC. Talks about the future often focus on data size. Titus pointed to one such talk by Mike Schatz of Cold Spring Harbor: “The next 10 years of quantitative biology”. (Also check out the latest big data  Cold Spring Harbor meeting, whose abstract deadline is August 22nd.) Sequencing …

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Data Notes: Dissecting the most boring buzzword ever

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By far one of the biggest concerns around Open Data is not whether we have the technology to enable researchers to make their data open but whether the cultural incentives are in place to make researchers freely share their data. Several publishers have recently started publishing ‘data journals’ or ‘data notes’. Is this latest publishing buzzword the answer to incentivising Open Data?

I try not to write in the first person (partly to avoid flashbacks of big red X’s from my high school essays) but this post—about something I myself have debated quite a bit—seems to demand it. As head of open data initiatives and policy here at BioMed Central, I’ve spent the last year questioning the need for ‘data notes’. …

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Implementing Reproducible Research: the Role of Publishers. An interview with Iain Hrynaszkiewicz, Peter Li, and Scott Edmunds


Implementing Reproducible Research, recently released by CRC Press and edited by Victoria Stodden, Friedrich Leisch, and Roger Peng, clearly describes the changes needed in science and publishing to help foster reproducible research.

With contributions from key leaders in computational science, such as Titus Brown, the book covers topics ranging from good programming practice and open source computational tools to the role of publishers in reproducible research.

Below is an interview with the authors of the chapter ‘Open Science and the Role of Publishers in Reproducible Research’, Iain Hrynaszkiewicz (Outreach Director at F1000), Peter Li (Data Organisation Manager at GigaScience) and Scott Edmunds (Executive Editor at GigaScience).


Your chapterOpen Science and the Role of Publishers in Reproducible

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BioMed Central rolls up its sleeves for citizen science

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OPAL Tree Survey staff briefing

Posted on behalf of Shreeya Nanda, Deputy Editor for Biology and Medicine, BioMed Central

At this year’s BMC Day, the once-yearly company bonding event, we got to be citizen scientists, participating in projects ranging from classifying cancer cells on a computer screen to venturing out into the unknown (not really, it was just a park in Vauxhall) to categorise trees. For some, conducting scientific research was a novel experience, for others it probably brought back memories (hopefully not painful ones) of previous lives in laboratories. But I think I can safely say that for all of us, it was an interesting and rewarding experience.

Citizen science, as the name suggests, is scientific research conducted by amateurs and non-professionals, and as a concept …

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