Guest posting: Many journals have determined that they can assist in data sharing

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Today we have a guest posting from F1000′s Iain Hrynaszkiewicz covering the topic of medical data sharing

One of the world’s most influential medical journals recently highlighted data sharing as an important issue to be addressed if we are to improve the quality of reporting of biomedical research. However, the journal may have overlooked strong and far-reaching support for data sharing in some publishing and research communities.

In an editorial published last month in JAMA, former Editor of the journal Drummond Rennie and its current Executive Managing Editor Annette Flanagin reported on the Seventh International Congress on Peer Review and Biomedical Publication in September 2013. Although criticized in 2009

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Q&A on dynamic documents

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At GigaScience one of our major goals is to take the scientific publishing beyond dead trees and static PDFs to a more dynamic and interactive process, much like science itself has embraced the Internet to become more networked and data driven. One way we have done this is by enabling the histories and analyses from papers to be visualized and executed through our GigaGalaxy server (see our recent posting on this), but on top of integrating workflows into our papers through citable DOIs, the papers themselves can be generated (and subsequently reproduced) in a similar manner using a number of tools that allow …

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CARMEN, reproducible research and push-button papers

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Researchers release a treasure trove of data on the developing retina, pushing the boundaries of neuroscience publishing by presenting it dynamically and reproducibly.
A new paper in GigaScience today demonstrates a major step forward for reproducible research and public data-sharing in the neurosciences with the publication and release of a huge cache of electrophysiology data resources. Important for studying visual development, many groups have been using multielectrode array recordings to look at developmental changes and the effects of various genetic defects on the spontaneous activity of the retina. We’ve written previously about the difficulties in sharing neuroscience data, …

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Having a finger on the pulse of data citation

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Endorsing Data Citation
Nicely timed for the Data Citation Principles workshop at the IDCC meeting in San Francisco yesterday, the finalized Joint Declaration of Data Citation Principles has just been posted on the Force11 website. We of course endorse these, as data citation is an area we have been promoting and practicing since our formation, using it as a mechanism to incentivize and credit the early release of data from data producers. Most of the challenges have been cultural rather than technical, and despite some setbacks (for example from Nature

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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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