Continuing our #usegalaxy series at the 2014 Galaxy Community Conference

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The upcoming 2014 Galaxy Community Conference (GCC2014) has just opened early registration, and following from our series announced at the last meeting we are renewing our call for papers for our special thematic focused series on studies utilizing large-scale datasets and workflows. For those not part of their large and rapidly growing user base, Galaxy is an open, web-based platform for data intensive biomedical research allowing users to reproduce and share analyses. GigaScience, with its aims to increase reproducibility and transparency of research has been utilizing our own GigaGalaxy server, enabling the hosting and implementation of Galaxy-based …

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Rewarding Reproducibility: First Papers in our Galaxy Series utilizing our GigaGalaxy platform

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Push the button! GigaScience moves toward more interactive articles

Research articles are being published with increasingly large and complicated supporting datasets, together with the software code used in analyses of the data. However, there is a growing number of studies reporting the inability to reproduce previously published findings which may, at least in part, be responsible for the increasing rate of retractions that Bjorn Brembs has calculated will overtake the number of papers published some time in the mid-2040s. Furthermore, there is an awareness of the “reproducibility gap” within the scientific community, with Francis Collins of the NIH

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GigaScience goes CC4. A handy cut out and keep guide to our licenses

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We want you to use our stuff
We get many queries regarding the policies and licenses associated with our content and supporting data, and as our co-publishers BioMed Central have just announced the migration of their licenses (including ours) to the newly released version 4.0 of the creative commons CC-BY attribution license, we thought it would be a good opportunity to clarify our policies in an easier to understand manner than having to trawl through our editorial policy pages. Puneet Kishor the Science and Policy Data manager at Creative Commons gives a great overview

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Moving pictures of the Microbiome in GigaScience

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Visualizations are becoming increasing important to graphically illustrate, understand, and glean insight from the explosion of larger and larger datasets in this supposed era of “big data”. Microbial ecology and the study of the microbiome is revolutionizing how we look at health, microorganism diversity and ecological interactions, but these studies are proving challenging to deal with the ever-expanding numbers of specimens sampled. New analysis tools are required to relate the distribution of microbes across these datasets, and integrate rich and standardized contextual metadata to understand the biological factors driving these relationships. Ambitious “megasequencing” projects such as the Earth Microbiome Project (EMP), which aims to construct a microbial biomap of the …

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Calling all papers for the 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)

Last July, GigaScience and the organisers of the Automated Function Prediction special interest group at ISMB announced an upcoming series on Automated Function Prediction. This is 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. Check out our write-up covering some of the talks at the meeting.

As announced at the meeting, the second round of the critical assessment of functional annotation (CAFA2) is currently taking place. The aim of CAFA is to …

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A GigaGathering at ICG8 in the era of big data and crowdsourcing

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As the GigaScience journal moves from strength-to-strength, with that comes the expansion of the editorial and data management teams that are now spanning three continents – and what better way to meet than at the 8th International Conference on Genomics (ICG8) in Shenzhen, China, co-organised by the BGI and GigaScience. Held at the Thunderbirdsesque Vanke International Conference Centre in the popular seaside resort of Dameisha, this year’s meeting covered a range of topics including new innovations and technologies, big data management, crowdsourcing, animal and crop genomics, as well as informatics and metagenomics, to name a few.

George Church was the highlight on the first day, who not surprisingly, gave a fascinating keynote on his amazing technology developments …

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Release the Bats! New Halloween #opendata treat in GigaDB

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As big proponents of Open Data, on top of the many diverse datasets associated with GigaScience papers in our integrated GigaDB database, we are continuing to fill it with datasets produced by our BGI hosts. As a special Halloween treat, today we’ve added three bat genomes to the database: Brandt’s bat (Myotis brandtii), the Black Flying Fox (Pteropus alecto) and the Mouse-eared bat (Myotis davidii). While these species have been available in the SRA been since publication in Science and Nature Communications, we have …

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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!

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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

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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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