Posts tagged: Open Data

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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Can you show us that again please?


For almost thirty years, David Stern has been obsessed with the fact that male fruit flies ‘sing’ to females. His work on this problem, published today in BMC Biology, has got him thinking about reproducibility in science. In this guest post, he sets out his prescription to help scientists check whether research results are reliable

As an undergraduate at Cornell in 1985, I looked for a research problem that combined my interests in genetics, evolution, and behavior. Kyriacou and Hall had recently reported that the period gene, which regulates circadian rhythms, also controlled a rhythm of fruit fly courtship song and that evolution of period explained a species difference in this courtship song rhythm. This seemed …

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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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Contamination and the 1000 Genome Project

Human genome

According to a paper published today in BioData Mining, contamination of genomes from the 1000 Genome Project was found in a significant amount of raw data pulled from the project. 

The author William Langdon analysed the available raw data from the project (50 billion DNA measurements) and found that some of the data did not match human genomes (around 7%). These were in fact Mycoplasma genomes.

Contamination of samples is well known in genomics, especially in certain cases such as with Nematoda and related animals. Such animals often ingest the cells of their hosts. Even with free-living animals, it is not unheard of for samples to become infected with cells from ingested food. It’s also particularly common …

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How should citizen science be published? A debate at Citizen Cyberscience Summit 2014

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Fraxinus - each player contributes small but useful data helping to understand the cause and susceptibility to the ash dieback fungus

Citizen science – the public participation in gathering data for scientific studies – is certainly not new, but facilitated by the ease of sharing information online, the opportunities for the public to engage in scientific data collection have increased in recent years. Zooniverse, one of the most successful platforms facilitating citizen science experiments, recently announced that they now have over 1 million registered users (this map shows how geographically diverse they are), quite an impressive milestone to reach in just seven years.

But what are the implications of publishing scientific studies which, by definition, rely on the engagement of a broad group of participants?

BioMed Central is organising a panel discussion at the Citizen Cyberscience Summit to discuss this question, rounding off the second day of the conference in London this Friday.

Our Medical Future

Pills with sensors

Health and healthcare were a prominent theme of this year’s World Economic Forum in Davos, and one of the first sessions took a look into our medical future.

Notably, the leaders of the session did not include a doctor/physician. The moderator Lionel Tarassenko is a professor of electrical engineering at Oxford, and speakers were genomics researcher Professor Steve Cole (UCLA) and Andrew Thompson, CEO of Proteus Digital Health. Between them, they conveyed a powerful vision of digital health monitoring in our everyday lives that will empower preventative and personalized medicine.

Lionel Tarassenko explained how his previous work for Rolls Royce has fueled his ideas for developing digital health care. Their jet engines are continuously monitored as they fly …

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The Force 11 Resource Identification Initiative and the Article of the Future


With the literature available to researchers growing—indeed, in the last decade the amount of articles published increased by around 44%[i]—the way in which researchers are able to consume that literature becomes increasingly important. Readers need ways to quickly find what research is relevant to them. For example, say I want to find all the literature behind a specific research resource (eg, software, databases, antibodies, model organisms, etc). Doing this would be timely and inaccurate at best. Why? Because they’re not necessarily tracked or machine-readable. And because researchers don’t consistently or uniformly cite these resources.

In an era of “big publishing” and the Web, we are undergoing a cultural shift in the way we communicate science and interact with “the …

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Threaded Publications: one step closer

Threaded Publications

“It is difficult to make informed decisions if publication bias and selective reporting are present”
World Health Organization

For years, researchers have drawn attention to this, highlighting discrepancies between protocols submitted to research ethics committees and those reported in the results papers, issues concerning statistical power, and the difficulty in identifying unpublished studies. Indeed, it was concerns like these that lead to most major medical journals making registration of clinical trials a prerequisite for publication.

However, even for those clinical trials that have been registered, it can be difficult to track down related content. Not all journals publish the trial ID in the body of the article; therefore, although a results article may cite …

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Moving Forward: BioMed Central’s open access license is being updated to CC-BY 4.0


Back in August we announced that all data published in BioMed Central articles would be published under the Creative Commons CC0 public domain waiver for data. At that time, we also announced our intention to upgrade the attribution component of BioMed Central’s license agreement from CC-BY 2.0, which we introduced as our standard license in 2004, to the latest  license version, CC-BY 4.0. This improved and updated version of the CC-BY license was released on 25 November 2013. We are now able to confirm that all BioMed Central, Chemistry Central, and SpringerOpen articles submitted on or after 3 February 2014 will be published, if and when editorially accepted, under the updated CC-BY 4.0 Creative Commons

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