Author profile
Scott Edmunds
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. […]
Enter the GigaScience Prize Track at ICG-12
Scott Edmunds - May 29, 2017
Call for Submissions – Win Prizes and Join us in Shenzhen for ICG-12 Being co-published by BGI and based at their Hong Kong office we are regular participants at their yearly ICG (International Conference on Genomics) conference in Shenzhen. Since the very first meeting in 2006, ICG has grown to become one of the most […]
Guardians of the Galaxy Workflow
Scott Edmunds - April 28, 2017
While the Guardians of the Galaxy film franchise has just released its second film, the GigaScience Galaxy series has just published its 10th, 11th and 12th papers. And all without the need of expensive CGI, although we do have our GigaGalaxy server on standby for additional computational support. For those not part of their large […]
Getting the Buzz on Bee Parasites. Author Q&A with Tatsuhiko Kadowaki
Scott Edmunds - February 24, 2017
The decline of global honeybee populations are a major environment concern, because of their vital role in our food systems and pollination of flowering plants. Twenty first century ‘Omics is coming to the rescue, and published in GigaScience this week is an article that presents the genome and proteome of a mahor threat to bee […]
Ginkgo genome fills an evolutionary hole
Scott Edmunds - November 25, 2016
New in GigaScience is an article that presents the genome sequence of Ginkgo biloba, the oldest extant tree species. The research was carried out by a team of scientists at BGI, Zheijiang University and the Chinese Academy of Sciences, who tackled and analyzed an exceptionally large genome, totalling more than 10Gb. Ginkgo is considered by some as a “living fossil”, its form and structure having changed very little in 270 million years. Its unique position in the evolutionary tree of life means the ginkgo genome will provide an extensive resource for studying early events in tree development and evolution.
Personal Genomics Enters a New Phase
Scott Edmunds - October 11, 2016
Individual human genomes are diploid in nature, with half of the homologous chromosomes derived from each parent. The context in which variations occur on each individual chromosome has profound effects on the action and clinical importance of the genes on it, but this “haplotype” information has been mostly ignored in genomics research to date. A wealth of new data released from the Personal Genome Project via a new Data Note helps fill this gap by releasing the largest set of high coverage whole human genome assemblies with experimentally determined haplotypes to date.
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.
Of big fish and small genomes. Ocean sunfish shines.
Scott Edmunds - September 12, 2016
The genome of the ocean sunfish (Mola mola), the world’s largest bony fish, has been just been published in GigaScience by researchers at A*STAR, Singapore, and China National Genebank. Here we talk to the researchers, including Nobel Laureate Sydney Brenner, on how the project came together, the slightly unusual sample collection, and how hope this work helps to provide insight into the fish’s extraordinary growth rate and unique body shape.
Guest posting: Building a PhenoMeNal metabolomics e-infrastructure
Scott Edmunds - July 19, 2016
David Johnson and the PhenoMeNal consortium have a guest posting on their efforts in building an open, community-supported, e-infrastructure for medical metabolomics data, and how they are seeking community feedback on the requirements for the data infrastructures needed.
#ISMB16: A Disney Coming of Age Tale.
Scott Edmunds - July 15, 2016
At Disney World infancy ends at 3, or at least that is the age children have to start purchasing tickets. It seemed appropriate to celebrate our 4th birthday there. Or at least at the #ISMB16 Computational Biology meeting that was held this week at the Walt Disney World Resort. Here we report on what happened and how we and the field have been growing up