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 …
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 …
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’. …
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 …
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 …
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, …
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 …
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 chapter ‘Open Science and the Role of Publishers in Reproducible …
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 …
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.