Tag Archives: reproducibility
Open Access Week 2021: GigaScience’s 10 Examples of Open
Scott Edmunds - October 29, 2021
For Open Access Week 2021 we look back over 10 of our favourite GigaScience papers providing examples of barriers we’ve tried to break for more open science.
Gigantum Joins the Giga Reproducibility Toolkit
Nicole Nogoy - June 2, 2021
Joining our Giga reproducibility toolkit is Gigantum, with a new paper being our first example using this platform for better collaboration, sharing and making reproducible research easier.
Changing the Culture of Data Management and Sharing: A Report on the NASEM Workshop
Chris Armit - May 26, 2021
The National Academies of Sciences, Engineering, and Medicine (NASEM) hosted the virtual workshop “Changing the Culture of Data Management and Sharing”. Here we have a write-up of the event.
GigaByte and River Valley Technologies push the boundaries of Executable Research Articles using Stencila and Code Ocean
Scott Edmunds - February 25, 2021
Today GigaByte publishes its first Executable Research Article (ERA), using technology from Stencila and Code Ocean to showcase interactive and executable versions of the figures.
Reproducible Classification. Q&A on ShinyLearner & the CODECHECK certificate, pt. 2
Scott Edmunds - April 8, 2020
This week we showcased a new way of peer reviewing software, testing code in an independent manner and providing a CODECHECK “certificate of reproducible computation” when the results in the paper can be reproduced. We’ve written a post on the CODECHECK process featuring a Q&A with CODECHECK founder Stephen Eglan, and here we’ll provide a follow […]
Certified Reproducibility. Q&A on ShinyLearner & the CODECHECK certificate, pt. 1
Scott Edmunds - April 7, 2020
Out today in GigaScience is ShinyLearner, a new tool to make it easier to perform benchmark comparisons of classification algorithms. This tool stands out by making this process super systematic and reproducible, and despite needing to interface with many different libraries and languages it uses software containers (and a CodeOcean demo) so end users don’t […]
iMicrobe: Fostering Community-Driven Science and Data Discovery. Q&A with Bonnie Hurwitz
Nicole Nogoy - August 2, 2019
In this data-driven era, research is faced with new challenges, from sharing, storing and accessing data, including how to better integrate data to answer big questions in science. With many data repositories available, it is hard to maintain them all – some repositories are forced to close – meaning loss of access to invaluable datasets. […]
GigaBlog meets Gigantum: Guest Post from Tyler Whitehouse, Dean Kleissas and Dav Clark
Nicole Nogoy - June 20, 2019
At GigaScience as our focus is on reproducibility rather than subjective impact, it can be challenging at times to judge this in our papers. Targeting the “bleeding edge” of data-driven research, more and more of our papers utilise technologies, such as Jupyter notebooks, Virtual Machines, and Containers such as Docker. Working these tools in to […]
Meet the GigaScience ICG Prize Winner, Pt. 2: Lisa Johnson Q&A
Scott Edmunds - December 14, 2018
Yesterday we published the winning paper of the second GigaScience prize, with additional detail and coverage in GigaBlog describing why we and the judging panel found it so novel. This was an impressively case study in reproducibility, reassembling & reannotating around 700 microbial eukaryotic transcriptomes to demonstrate this approach can aid in revealing new biologically relevant […]
Research Parasites Wanted. Q&A with Casey Greene & Brian Byrd
Scott Edmunds - September 14, 2017
As a journal focussed on open science we are big promoters of research parasites (and research on parasites), and try to feeds them with open data and tools. It is therefore appropriate this is the second year GigaScience has supported and sponsored the Research Parasite awards. In one of our Q&As, organisers Casey Greene and […]