The cyber-centipede: giving online species descriptions a leg up

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The rate of species extinction has lent increasing urgency to the description of new species, but in this supposedly networked “big data” era the process of cataloging the rich tapestry of life has changed little since the time of Linnaeus. Fortunately, this process is finally being dragged into the 21st century, as the procedure of describing animal species at last entered the electronic era last year with the acceptance of electronic taxonomy publication and registration with ZooBank, the official registry of the ICZN. Concerned with growing disappearance rates, scientists have been forced towards a so called turbo taxonomy approach, where rapid species description is …

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Open Data For The Win!


Depositing data in GigaDB helps authors win BMC Open Data Award by boosting confidence in unexpected research findings
Last night at the Beyond the Genome conference in San Francisco, researchers were presented with this year’s BioMed Central Open Data Award for their work demonstrating that DNA methylation occurs in the parasitic worm Trichinella spiralis, a human pathogen also known as “pork worm” due to it being found in undercooked pork products. One of the challenges in getting researchers to put in the time and effort to make their data available in a curated and usable form is a perceived lack of incentives. Journal …

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Extended Q&A with Assemblathon2 Author Keith Bradnam


A lot has already been written about last months Assemblathon2 paper in GigaScience (see the growing list of articles here), but for the box-set completists interested in squeezing every last bit of insight into the project and how it was put together, there was a lot of additional material left over from the recent Biome Q&A with Keith Bradnam that we thought it could be useful to post in a (hopefully final) blog posting. Keith is a project scientist in the Korf lab at UC Davis where he has juggled investigating intronic-based signals in gene expression and running the Assemblathon. This is …

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Save the trees. Play facebook games.

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Gamers to join ash dieback fight-back
Next time you sit next to someone on the train playing a game on their smartphone don’t be too dismissive. They may be harnessing the most state of the art genomics technology in the fight to save Northern Europe’s woodlands from destruction. We are obviously not talking about Candy Crush, but a new and addictive Facebook puzzle game called “Fraxinus”, developed by scientists from The Sainsbury Laboratory in Norwich and the gaming company Team Cooper. The game uses real genetic data from the fungus that is causing the devastating ash dieback disease, and from …

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More on our ISMB workshop: What Bioinformaticians need to know about digital publishing beyond the PDF


Big Data Publishing (credit Jenny Cham, CC-BY)
As mentioned in our previous posting, on top of the many great talks and sessions we attended at ISMB in Berlin last month, we were kept even busy helping to organize and present in a special Beyond-the-PDF inspired “What Bioinformaticians need to know about digital publishing beyond the PDF” workshop. Most of the heavy lifting has to be credited to the hard work of Marco Roos, but the other organisers included Oscar Corcho, Carole Goble, Barend Mons, Jun Zhao and Erik Schultes, and we had a ridiculously overqualified …

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Bioinformaticians breaking down barriers in Berlin

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Open Science flourishes at BOSC and ISMB
It’s been a busy couple of weeks for GigaScience, with our 1st birthday, publication of a special anniversary print issue sponsored by Aspera, and publication of the (unusually reviewed) Assemblathon2 paper. These all spanned and were coordinated with the ISMB meeting in Berlin, the yearly gathering of the computational biology community. GigaScience was present through the pre-conference SIGs (particularly BOSC and AFP), as well the main conference, co-organizing and speaking at a special …

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Genome assembly in the spotlight

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Biggest ever contest to put genome assemblers through their paces
If you haven’t caught it yet, the largest systematic assessment the process of genome assembly carried out to date has been published this week in GigaScience. The second Assemblathon competition saw 21 teams submit 43 entries based on data from three different unassembled parrot, cichlid fish, and boa constrictor genomes sequenced using three different technologies. Ten key metrics are outlined, based on over 100 different measures for each assembly, and they focus on different aspects of an assembly’s quality.

The paper has already generated a lot of coverage, particularly on the unusual peer review process. Assemblathon2 was initially submitted to a …

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GigaBirthday at ISMB


GigaScience reaches its first anniversary of publication, and achieves several milestones in changing how life science research is published

One year on from our launch, we are unveiling new features and functionality at the Intelligent Systems for Molecular Biology (ISMB) meeting at the ICC in Berlin (pictured) this week. As well as a print issue celebrating the best of the last year, we are announcing new features and tools, along with a new data analysis platform, GigaGalaxy. GigaGalaxy is an online platform that supports the reproducibility of data analyses. It provides a means to share computational tools and workflows that further document and reproduce data analyses reported in papers …

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#usegalaxy lights up northern skies


Galaxy shines in the land of the midnight sun
Immediately after beer, mussels and genomics at ICG-Europe in Ghent (see BGI’s write-up of the event), last week was a blur of eye-wateringly expensive alcohol, brown cheese and reproducible research at the Galaxy Community Conference in Oslo. Now in its 4th year, and the second year we have attended (see the blog and Genome Biology meeting report from last years meeting in Chicago), GCC 2013 was bigger and better than ever. Tripling in size since the first meeting, the over …

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Automated function prediction – call for papers for a special series


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

To tie in with the upcoming Automated Function Prediction Special Interest Group (AFP-SIG) at the ISMB/ECCB 2013 meeting in Berlin, GigaScience and the organisers are launching a call for submissions to a thematic series of research from the meeting and beyond highlighting (but not limited to) function prediction using sequence-based methods, function from genomic information,  molecular interactions, structure, use of combined methods, and phylogeny-based methods. The meeting will also kick off the second Critical Assessment of protein Function Annotation (CAFA) challenge, in which various function prediction algorithms will be tested for accuracy.

The explosion in genomic …

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