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

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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CARMEN, reproducible research and push-button papers

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Researchers release a treasure trove of data on the developing retina, pushing the boundaries of neuroscience publishing by presenting it dynamically and reproducibly.
A new paper in GigaScience today demonstrates a major step forward for reproducible research and public data-sharing in the neurosciences with the publication and release of a huge cache of electrophysiology data resources. Important for studying visual development, many groups have been using multielectrode array recordings to look at developmental changes and the effects of various genetic defects on the spontaneous activity of the retina. We’ve written previously about the difficulties in sharing neuroscience data, …

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Having a finger on the pulse of data citation

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Endorsing Data Citation
Nicely timed for the Data Citation Principles workshop at the IDCC meeting in San Francisco yesterday, the finalized Joint Declaration of Data Citation Principles has just been posted on the Force11 website. We of course endorse these, as data citation is an area we have been promoting and practicing since our formation, using it as a mechanism to incentivize and credit the early release of data from data producers. Most of the challenges have been cultural rather than technical, and despite some setbacks (for example from Nature

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Continuing our #usegalaxy series at the 2014 Galaxy Community Conference

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The upcoming 2014 Galaxy Community Conference (GCC2014) has just opened early registration, and following from our series announced at the last meeting we are renewing our call for papers for our special thematic focused series on studies utilizing large-scale datasets and workflows. For those not part of their large and rapidly growing user base, Galaxy is an open, web-based platform for data intensive biomedical research allowing users to reproduce and share analyses. GigaScience, with its aims to increase reproducibility and transparency of research has been utilizing our own GigaGalaxy server, enabling the hosting and implementation of Galaxy-based …

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