Guest Blog: Challenges and opportunities with sharing neuroimaging data

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Here we present a guest blog by our Editorial Board Member Russell Poldrack, Professor of Psychology at Stanford University, who highlights the challenges and opportunities surrounding imaging data to enable the neuroscience community to “stand on the shoulders of giants”.

The sharing of neuroimaging data is an idea whose time has finally come, but many challenges remain.  Foremost is the incentive problem: Why should a researcher take the time to organize their data for sharing when they could spend the same time working on a new study or paper?  Related is the credit problem: How will a researcher receive credit for having shared their data?  In addition, there are technical challenges …

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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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All systems go at ICSB 2014 and the Great GigaScience and Galaxy (G3) workshop

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The 2014 International Conference on Systems Biology (ICSB) was hosted in Australia’s most livable city and event, sport, culture and food capital – that is Melbourne, with GigaScience being proud to be one of the media partners. Stem cell biology was a major theme on the first day, and kicked off to a strong start with Huck Hui Ng (Executive Director  of the Genome Institute of Singapore) giving a great overview of stem cell systems biology. Ng explained how his lab has set up high-throughput capabilities to further understand stem cell pluripotency. Ng’s lab has been able to show that maintenance of human embryonic stem cell stability is governed by – proteins, TFs and co-factors, mediators of …

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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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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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