Tag Archives: reproducible research
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 […]
Reprocessing the Microbial Genomic Goldmine: Winner of the ICG13 Prize
Scott Edmunds - December 13, 2018
Out today is the winner of our ICG13 Prize, presenting work that can aid in revealing new biologically relevant findings and missed genes from previously generated transcriptome assemblies. Teaching old data new tricks, and maximising every last nugget of information from previously funded research. Here we present some insight into why the reviewers and judges […]
CUDDELing up to metabolomics in Hong Kong
Peter Li - January 22, 2018
As mentioned in our Happy New Year blog post, one of the highlights in 2017 was a second GigaScience hackathon workshop which we held in November last year in our Hong Kong BGI office. Funding for this workshop came from a project we have called CUDDEL which was awarded a grant by the BBSRC from their China […]
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 […]
Data Intensive Software Publishing & Sailing The Code Ocean. Q&A With Ruibang Luo.
Scott Edmunds - June 27, 2017
GigaScience is always trying to push the boundaries of how we disseminate reproducible research, and to adapt to the challenges of dealing with experiments become more data-intensive. We now showcase a new reproducible research platform we’ve been testing called Code Ocean, and have a Q&A with our Author Ruibang Luo on his experiences using it. […]
Remember Remember, It’s Neuro-November!
Nicole Nogoy - November 1, 2016
Halloween may be over, but this November GigaScience will be continuing to fight the zombie (paper) apocalypse and binge on sweet sweet brains (research outputs).
Guest posting: Conda as a new standard for Galaxy tool dependencies
Scott Edmunds - September 20, 2016
The Galaxy community is one that shares similar reproducibility goals with GigaScience, having a computational platform that allows users to share workflows, histories and wrapped computational tools in an easy-to-use and open source interface. Björn Grüning and The Intergalactic Utilities Commission of Galaxy have a guest posting here to announce new changes that will make development and presentation of tools and pipelines through Galaxy even more reproducible and usable.
The lowest common denominator: marketing science with jIF
Scott Edmunds - July 8, 2016
Our Editor in Chief Laurie Goodman gives her thoughts on the journal impact factor (jIF), and how we need to move beyond shallow, untransparent, gameable, out-of-date proxies that promote bad scientific practices.
Of Parasites & Protocols, Part 3. Author Q&A with Tony Papenfuss
Scott Edmunds - June 16, 2016
Following our announcement this month of a new collaboration and integration with protocols.io, we’ve gone into more detail on the first two papers that have utilised this open access repository of scientific methods and collaborative protocol-centered platform. To give some insight into his work, we have one of our author Q&As with Associate Professor Tony Papenfuss, lead author of our scabies genome paper.