Posts by Scott Edmunds

GigaScience editor and data nerd working at the BGI and based in Hong Kong.

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Follow author on Twitter: @SCEdmunds

Q&A on dynamic documents


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


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


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


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


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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Release the Bats! New Halloween #opendata treat in GigaDB



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!


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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