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

A Flock of Bird Data Comes to Roost

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In the long history of humankind (and animal kind too) those who learned to collaborate and improvise most effectively have prevailed.

—Attributed to Charles Darwin

In 1839 Charles Darwin published his famous account of the 5-year second voyage of the HMS Beagle, describing the flora and fauna he encountered surveying South America and circumnavigating the globe, including the famous Galápagos finches that helped develop much his theory of evolution. Providing his descriptions of these species in this 175 year old work, as well as donating his collected specimens to the Zoological Society of London, it was not until 20 years later, in the 1859 “On the Origin of Species” that the true implications of this work was …

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Publishing our first virtual box of delights to aid the fight against heart disease

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Sheer Heart Attack
Diagnosis is key to beginning treatment for preventing coronary heart disease, the most common cause of heart attacks. One useful tool in the fight against this leading killer is magnetic resonance imaging, which allows the direct examination of blood flow to the myocardium of the heart. However, for this perfusion analysis technique to be the most effective requires compensation for the breathing motion of the patient, which is done using complex image processing methods. Thus, there is a need to improve these tools and algorithms. The key to achieving things is the availability of large publicly available MRI datasets to allow testing, optimization and development of …

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Secure Genetic Data Moves into the Fast Lane of Discovery

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Take a ride down chromosome highways with a novel web-based platform that allows sharing of private genetic data while maintaining privacy through a colourful dynamic visualization tool.

The Human Genome Project offered new hope that discovering the genetic determinants which mediate chronic disease susceptibility would lead to new avenues for drug development and targeted therapy, yet over decade later the is disappointment that very few gene screens have made it into the clinic to inform and improve treatment. Getting the most out of the explosion of human genetic data has been difficult due to the massive size of the data produced, as well as the challenges in balancing the need to protect patient privacy with the need to be …

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Uncovering the tangled roots of plant evolution

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Using big data to understand the tree of life
New work just published in the Proceedings of the National Academy of Sciences and GigaScience reveals important details about key transitions in the evolution of plant life on our planet, and present a huge cache of computational results, data and tools for plant biologists.

In closing the Origin of Species, Darwin described a “tangled bank, clothed with many plants of many kinds”, and this metaphor is apt for our still tangled understanding of how the key branches of the tree of life fit together, particularly the plant kingdom. From strange and exotic algae, mosses, ferns, trees and flowers growing deep …

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Guest Blog: The 2014 Ebola Epidemic: Approaches and resources to slow the spread of infection

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The Ebola pandemic presents one of the most terrifying world health crises in modern times, with devastating consequences in Western Africa [as this goes to press there are now over 10,000 infections and almost 5,000 deaths]. There is a vast amount of data on this crisis available in rapidly published articles and on the internet (check out PLOS Currents: Outbreaks in particular), including past and current numbers of infected; death and infection rates; predicted outbreak expansion; number of current and needed health care workers and treatment centers; required financial resources; and more. These available data can, and are, being used for a broad range of topics, for example a

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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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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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