Posts tagged: Open Data

Making Sense of Big Data: Standards in Genomic Sciences





Nearly 20 years into full genome sequencing, today the cost of sequencing a single genome, once a feat of only the well-funded, is ceasing to be a matter of discussion. Sequencing is merely data gathering for the biology. With this change, journals too have changed. Looking to publish scientific breakthroughs, many journals have stopped considering the sequencing of a whole genome a scientific advancement, or work worthy of publication. But as the cost of sequencing drops, the amount of data in public databases rapidly accumulates. And as with all big data, its great potential lies in its size. We need to be able to view genomes in comparison. Yet there is no contextualisation for this data: what methods were …

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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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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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National healthcare: The modern biomedical lab

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Brownstein et al

In 2009 Obama devoted $19 billion to healthcare innovation—innovation that was in its first instance quite rudimentary, the very digitisation of healthcare data. Now as the digitised healthcare data infrastructure grows both in the US and worldwide, what is the next phase of innovation?

The answer, from someone who works with researchers, is clear: a data dialogue between researchers and clinicians. Initiatives like the Global Alliance for Sharing Genomic and Clinical Data led by David Haussler are making strides toward doing this for treatment and research for cancer.

Last week I attended ISMB in Boston, where I saw one quantitative analyst (quant) who had similar ideas about better healthcare treatment through research and more data for research through healthcare. His …

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Building the Brain: The Human Brain Project and the New Supercomputer

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Upon this gifted age, in its dark hour,
Rains from the sky a meteoric shower
Of facts . . . they lie unquestioned, uncombined.
Wisdom enough to leech us of our ill
Is daily spun; but there exists no loom
To weave it into fabric.

Edna St Vincent Millay


“Big data”—once the domain of genomics—is now easily the domain of science in general. With new techniques to measure the brain and brain activity (fMRI, EEG, etc) gaining momentum, in the neurosciences tremendous amounts of data are now being generated. The question now is, as Millay points to, how to weave this data into meaning.

During London Technology Week Sean Hill, a co-director of the Human Brain Project (a European brain initiative …

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Free Swag and Other Things not to Miss Out on at ISMB


This week a few of us here at BioMed Central are off to Boston for ISCB’s annual ISMB conference and its Special Interest Group (SIG) meetings. First thing’s first: We’ll be giving away cool swag like our new Bruce Lee/Kill Bill inspired GigaScience Open Data tshirts. Our 8GB GigaPanda USB drives will also be making a repeat appearance.

Where can you get these? We’ll be at booths #419 and #420 and would love to chat to you about open peer-review and our journals Biology Direct and GigaScience or some of our informatics journals like BMC Bioinformatics, Journal of Biomedical Semantics, and BioData Mining. GigaScience will be celebrating their second birthday at the meeting, …

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