Faster, Dataset! Kill! Kill!

Scott Edmunds on June 7, 2013 at 10:58 am - 0 Comments

The speed of data
Last week was the Bio-IT World Asia meeting in Singapore, and while we didn’t attend this year (see last years conference report in Genome Biology), our editorial board member Tin-Lap Lee presented on the GigaGalaxy server that we have been collaborating with him on (see slides). Also timed for the meeting, Aspera made a press release on our recent adoption of their suite of software products to provide authors, reviewers, and users with the tools to upload and download the extremely large data sets that accompany manuscripts at maximum speed. You …

The difficulties sharing neuroscience data: can data publishing help?

Scott Edmunds on May 9, 2013 at 2:25 pm - 1 Comment

Last week we published our first neuroscience data note containing 10GB of fMRI data hosted and integrated into the paper by a DOI to our GigaDB database. While we have published a number of genomics datasets and data notes (see the Puerto Rican Parrot genome data note and its associated data DOI), this is a nice example of us providing a home for “orphan data”, the long tail of data types without community agreed curated repositories. Sharing of data enables re-use and new work to be created, all goals and reasons why we …

Giga-Galaxy moves into the metabolomics universe

Peter Li on May 3, 2013 at 1:32 am - 0 Comments

Sophisticated computational analyses must be performed on metabolomics data in order to measure the abundances of the metabolites. However, this typically requires expert knowledge in computer programming and biostatistics, restricting the usefulness of metabolomics to specialised laboratories. Thanks to funding from the UK’s Natural Environment Research Council, this project will develop a software platform based on Galaxy to make it much easier for non-specialist scientists to analyse their metabolomics datasets.

As the first metabolomics project in the recently announced Joint BGI-University of Birmingham Environment & Health Centre, the funding will enable Rob Davidson, a post-doctoral researcher from Mark Viant’s research group at the University’s School of Biosciences, to travel to Hong …

Genetics and open access publishing meets Chilli Crab

Scott Edmunds on April 17, 2013 at 7:15 am - 0 Comments

Singapore – a wonderful city of diverse cultures and culinary affair, is not just about the infamous chilli crab or signature cocktail, Singapore Sling, but from the 13-19 April the vibrant country plays host to one of the largest meetings in genetics and genomics. The 2013 Human Genome Meeting/International Congress of Genetics (HGM/ICG) meeting is the first of its kind in Asia – bringing together a genetics congress that has been held every five years since 1899 with the young upstart genomics experts from HUGO (the Human Genome Organisation), the 2013 meeting brought together over 1000 scientists from around the world at the Marina Bay Sands Convention Centre (a favourite …

Call for papers for a special GCC2013 Galaxy series

Scott Edmunds on April 5, 2013 at 8:15 am - 1 Comment

The 2013 Galaxy Community Conference (GCC2013) and GigaScience are today announcing a call for papers for a special thematic focused series on studies utilizing large-scale datasets and workflows. Galaxy is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. GigaScience, with its aims to increase reproducibility and transparency of research has just launched its own Giga-Galaxy server, enabling the hosting and implementation of Galaxy-based workflows and methods. To see examples of how this works, see the slides from our flashtalk at the …

Q&A with Xin Zhou, author of our insect “squishome” paper.

Scott Edmunds on April 2, 2013 at 9:45 am - 1 Comment

Following from our previous blog posting, here we profile and interview Dr Xin Zhou, lead author of our recent “squishome” insect goo metabarcoding paper. This NGS (next generation sequencing)-based work has already generated a lot of interest (see this write-up in Wired and this blog posting for nice examples), and here Dr Zhou gives more insight into the potential for the technique in studying biodiversity, as well as some of the quirky findings his team made validating the technique behind their laboratory in China.

Dr Xin Zhou is Director of the Environmental Genomics research group at Read more

New in GigaScience: the Squishome

Scott Edmunds on March 27, 2013 at 5:33 am - 2 Comments

Insect goo aids biodiversity research
Apologies to Jonathan Eisen (see Badomics in the journal), but today in GigaScience we publish a new “squishomics” approach for assessing and understanding biodiversity, using the slightly wacky sounding method of combining DNA-soup made from crushed-up insects and the latest sequencing technology. This bulk-collected insect goo has the potential to rapidly and cheaply reveal the diversity and make-up of both known and unknown species collected in a particular time and place.

Creepy crawlies are important indicators of diversity, as arthropods make up 80% of described species, and with an estimated only Read more

Tweenome on Film: Excellent Video on Crowdsourcing Killer Outbreaks

Scott Edmunds on February 21, 2013 at 10:07 am - 0 Comments

The BBSRC has just released an excellent video and article on crowdsourcing killer disease outbreaks very relevant to our recent commentary and blog postings on the OpenAshDB (the Ash Dieback disease crowdsourcing) project. Featuring interviews from Nick Loman and Lisa Crossman (also an author on our OpenAshDB paper), key contributors to the 2011 E. coli O104:H4 outbreak genome crowdsourcing effort, it gives a very good overview of the how our initial release of public domain genomic data via twitter helped kick-start a burst of crowd-sourced, …

Open Science versus Ash Dieback (and the Tweenome revisited)

Scott Edmunds on February 13, 2013 at 4:53 pm - 2 Comments

Bye Bye Bluebells
Bluebell woods, the dense carpets of violet–blue flowers found in ancient woodland are a spectacular and famous springtime sight in Britain, but this picture postcard scene is threatened as never before. Chalara fraxinea or ash dieback, a devastating fungal disease of ash trees has swept across northern Europe, and has now reached Britain, a country particular susceptible to its potential onslaught, as the estimated 80 million ash trees make up 30 per cent of woodland across the country. Ash trees particularly encourage biodiversity, as the tree branches are ideally spaced for light to pass through and let the bluebells and other species on …

Opening peer-review: our new paper on SOAPdenovo2 shows how it works

Scott Edmunds on December 27, 2012 at 5:09 pm - 3 Comments

With everyone in a reflective mood as the year comes to a close, one of the big scientific trends of 2012 has obviously been the high profile that open-access and more open methods of carrying out science has received. With the Elsevier boycott, UK Finch report, and launch of a number of innovative new schemes in publishing open-access research and data (including F1000 Research, eLife, PeerJ and of course GigaScience), 2012 has been talked of as the year of an “academic spring” that has started to shake up the centuries old, stuffy …