Posts by Scott Edmunds

GigaScience editor and data nerd working at the BGI and based in Hong Kong.

Visit author's website: http://www.gigasciencejournal.com/

Follow author on Twitter: @SCEdmunds

Community Genomes: From the Peoples Parrot, to “Crowdfernding”.

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Despite the precipitous drop in the price of DNA sequencing, global credit crunches have shrunk the science budgets able to properly take advantage of this. At least in the case of non-medical research. With acceptance rates for some of the major funding agencies in the US declining into single digit percentages, the research community needs to look to new ways of supporting the important work they do. One potential development to redress the balance is for scientists to cut out the middleman, and go appeal directly to the source of most scientific funds – the tax paying public. This more democratic approach to doing science rewards those who can engage directly with others. …

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Ain’t No Party like a Bring Your Own Data Party!

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Data Club is Gonna Show You How
As science is supposed to be about “standing on the shoulders of giants”, we all know sharing scientific data should be a good thing, but there are obviously large technical and cultural challenges holding things back. Things are a long way from the Jimmy Wales “Imagine a world in which every single person on the planet is given free access to the sum of all human knowledge” utopian dream, but some research fields (e.g. genomics) have done a better job making data available than others. Unfortunately sharing complicated scientific data usually isn’t as easy as just dumping it in a dropbox folder, and to be reused …

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Continuing the push beyond static documents. ISMB, and more on our “What Bioinformaticians need to know about digital publishing beyond the PDF2” workshop

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Boston 2014: More than a (Bioinformatics) Feeling
Following from our previous posting on BOSC, our birthday and the BMC Open Data award party in Boston, on top of having to dash between the many great talks and sessions at ISMB, we were kept even busier than usual helping to organize and present in a special Beyond-the-PDF inspired “What Bioinformaticians need to know about digital publishing beyond the PDF” workshop at the end of the conference. Coming in the year that Illumina are hoping to make human clinical genome sequencing affordable with new sequencing platforms, one noticeable trend this year was a larger …

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Bioinformatics, Birthdays, and Booze at Boston BOSC.

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Birthdays are always emotional. The GigaScience team are on their way back from the always jam packed ISMB meeting and its satellite SIGs. This year was a particularly event filled one, with our second birthday, the BMC open data award and drinks reception, and our “What Bioinformaticians need to know about digital publishing beyond the PDF2″ workshop all falling during the meeting. The SIGs were brilliant as always, and we had additional involvement this year, promoting and building on our AFP (Advanced Functional Prediction) series tied in with the SIG of the same name, and sponsoring BOSC (the Bioinformatics Open Source Conference) …

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New GigaDB Dataset: Ever wondered whats in your gut?

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A paper published in Nature Biotechnology today reveals the most comprehensive catalogue of genes in any single microbiome to date. While the roughly 20,000 genes in the human genome have been available for over a decade, the gene catalogue of the microbiome, our much larger “other genome” has to date been much more poorly understood and characterized. The team, including multiple authors from our host institution BGI, reveal a staggering 9.8 million genes in the collective non-redundant microbiome of ~1250 human gut microbiomes sampled worldwide to date.

The researchers combined metagenomic sequences from several previous large studies (MetaHIT, HMP and …

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Publish Data: Fight World Hunger

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3000 Rice Genome Sequences Made Publicly Available on World Hunger Day
Yesterday marked the publication in GigaScience of the first data from the 3,000 Rice Genomes Project, a collaboration between the Chinese Academy of Agricultural Sciences (CAAS), the International Rice Research Institute (IRRI), and BGI; as well as a commentary from the Directors of these institutes outlining the goals of this ambitious project. Our biggest Data Note to date, the publication and release of this enormous dataset in our GigaDB repository quadruples the current amount of publicly available rice sequence data, …

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The Early Earthworm Catches on to Full Data Release

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New research and data published in GigaScience and PLOS ONE provides complete open access to detailed 3D images of earthworms
To quote the American cartoonist Gary Larson: all things play a role in nature, even the lowly worm—but perhaps never in such a visually stunning way as that presented in two papers published last week in GigaScience and PLOS ONE. The work and data presented here provide the first-ever comparative study of earthworm morphology and anatomy using a 3D non-invasive imaging technique called micro-computed tomography (or microCT), which digitizes worm structures. This opens the possibility of scanning millions of specimens from museum collections, including extinct species, all of …

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The Latest Weapon in Publishing Data: the Polar Bear

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Being the largest land predator, the fearsome and enigmatic Polar Bear is seen by many as a powerful symbol to highlight of the threats to the environment through global warming. With a new publication on the Polar Bear genome out last week in Cell, they surprisingly are also an impressive example of how far data publication and citation has come in the last few years, and help debunk many of the negative arguments about the early release of datasets in this manner.

Providing a comparison of the genomes of polar bears and brown bears reveals that the polar bear is a much younger species than previously believed, having diverged from brown bears less than …

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Guest posting: Many journals have determined that they can assist in data sharing

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Today we have a guest posting from F1000′s Iain Hrynaszkiewicz covering the topic of medical data sharing

One of the world’s most influential medical journals recently highlighted data sharing as an important issue to be addressed if we are to improve the quality of reporting of biomedical research. However, the journal may have overlooked strong and far-reaching support for data sharing in some publishing and research communities.

In an editorial published last month in JAMA, former Editor of the journal Drummond Rennie and its current Executive Managing Editor Annette Flanagin reported on the Seventh International Congress on Peer Review and Biomedical Publication in September 2013. Although criticized in 2009

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Q&A on dynamic documents

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At GigaScience one of our major goals is to take the scientific publishing beyond dead trees and static PDFs to a more dynamic and interactive process, much like science itself has embraced the Internet to become more networked and data driven. One way we have done this is by enabling the histories and analyses from papers to be visualized and executed through our GigaGalaxy server (see our recent posting on this), but on top of integrating workflows into our papers through citable DOIs, the papers themselves can be generated (and subsequently reproduced) in a similar manner using a number of tools that allow …

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