Guest posting: Optical Mapping allows comprehensiveness and scalability that modern sequencing cannot provide

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Shedding light on what the Optical Mapping System can provide for genome analysis, here we present a guest posting from optical mapping pioneer and developer (and GigaScience Editorial Board Member), David C. Schwartz, who is a Professor of Chemistry and Genetics at the University of Wisconsin-Madison.

Taking the Google Maps approach: providing comprehensive, scalable worldviews

We use maps in our daily lives to get around town and to explore new places, and Google mapping software has almost perfected the ways we can do this. One appeal of Google maps is that you can seamlessly scale the resolution to suit the type of journey you’re plotting— use the street view for getting about town, perhaps to check buildings and …

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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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GigaScience – making open peer review more open: Q&A with Publons co-founder, Andrew Preston

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At GigaScience, one of our major goals is to improve transparency and reproducibility of research and one of the ways we do this is through open peer review. After the unusual “meta peer review” of our Assemblathon2 paper (see more in biome), we thought our peer review couldn’t get more open, but a small New Zealand-based start-up, Publons, who also happens to be the world’s largest open peer-review platform, approached and told us about their exciting, innovative approach that gives peer reviewers due credit for the work that they do. GigaScience peer reviewers can now get further recognised for their efforts through our partnership with Publons, which was recently announced via the BMC Blog. Following some of …

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Guest posting: Let’s crowdfund a fern genome that will blow your mind

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Following our efforts encouraging open-science projects, such as the community funded “Peoples Parrot” and OpenAshDieback, today we have a guest posting from Fay-Wei Li and Kathleen Pryer from the Department of Biology at Duke University covering a crowdfunding effort to sequence the Azolla genome.  They have already raised over $4,000 and have 25 days remaining until their deadline, so if you find the project interesting, there is time still to contribute on Experiment.com.

We need a fern genome.

Why? Because considering the 470 million year history of plants on land, most species belongs to bryophytes, lycophytes, ferns and gymnosperms, which eventually yielded to the infamous flowering plants 90 million years (Myr) ago. Ferns, the third largest of these five …

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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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From function “unknown” to “known”: First papers in our Automated Function Prediction series

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Editors: Mark Wass (University of Kent, UK), Iddo Friedberg (Miami University, Oxford, Ohio, USA), Predrag Radivojac (Indiana University, Bloomington, Indiana, USA)

A key to understanding life at the molecular level is based on accurate protein annotation at the functional level. However, due to the explosion of genomic sequencing data an inherent difficulty and expense exists to scale-up and biologically characterise the plethora of genes and proteins of unknown function – one problem of which is computational annotation of protein function. Genomic sequencing data coupled with high-throughput experimental data has created new challenges and opportunities for function prediction. The Automated Function Prediction Special Interest Group (AFP-SIG) brings together computational and experimental biologists, as well as biocurators, who are dealing with the …

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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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