Tagged: bioinformatics

Licensing bonanza in computational life sciences*   - Genomics Aotearoa

Genomics Aotearoa Sep 09, 2021

By Florian Pichlmueller (University of Auckland) and Christina Straub (ESR) . 2min read GPL, MIT, BSD, CC – no they’re not a secret vocabulary, these are in fact acronyms for open source licenses that allow code to be freely used, modified and shared. And there are many more – take a look at the open source initiative to see … Read More

Understanding life in our waterways through metagenomics - Genomics Aotearoa

Genomics Aotearoa Sep 03, 2021

By Michael Hoggard and Carmen Astudillo Garcia, University of Auckland The rapid development and extraordinary cost reductions of next-generation sequencing technologies has greatly increased data on the functioning of complex microbial communities. Although relatively new, metagenomics has already dramatically influenced our understanding of the microbial tree of life and the known virosphere via the genomic traces of organisms and viruses … Read More

Where are all the four-leaf clovers? And what does that have to do with learning to code? - Genomics Aotearoa

Genomics Aotearoa Mar 30, 2021

By Monica Vallender, Master’s student with AgResearch Invermay and the University of Otago. A few months ago, while home for the Christmas break, my mother – out of the blue – turned to me and asked, “what made you actually decide you wanted to go to university and study science?” Shocked and never thinking that I would someday have to … Read More

Containers for reproducible bioinformatics research - Genomics Aotearoa

Genomics Aotearoa Aug 12, 2020

By Aleksandra Pawlik, Ngoni Faya, Joseph Guhlin, Megan Guidry, Tom Harrop, Dinindu Senanayake Rapid development of computational bioinformatics tools mean we can more easily push research boundaries. However, it comes at a cost. The complexity of the software chain that needs to be installed and configured to run advanced workflows results in researchers spending hours, if not days, trying … Read More

Data analysis skills are in hot demand – what should we be doing about it? - Genomics Aotearoa

Genomics Aotearoa Jul 29, 2020

By Associate Professor Mik Black, Department of Biochemistry, University of Otago The increased availability of complex biological data sets means that analysis and computation are becoming critically important skills for New Zealand’s future scientists. Because of this, we need to be doing everything we can to help our students develop these skills, to better prepare them for large-scale data analysis … Read More

A random bioinformatics career walk … and how Genomics Aotearoa is helping researchers be a little less scared of the “command line” - Genomics Aotearoa

Genomics Aotearoa Jan 30, 2019

Dr Alana Alexander A “random walk” is a mathsy term for a path strung together with a bunch of random steps (not unlike trying to walk my stubborn St. Bernard cross on a leash). Despite being a bioinformatician (which folks often think means “also a maths wiz”), my maths is (unfortunately) not great. Therefore, I mention random walks not because … Read More

Solution to 50-year-old mystery could lead to gene therapy for common blood disorders - News

Jean Balchin Apr 06, 2018

In a recent study published in the journal Nature Genetics, UNSW Sydney-led researchers have used CRISPR-gene editing to introduce beneficial natural mutations into blood cells to boost their production of foetal haemoglobin. This study solves a 50-year-old mystery about how these mutations operate and alter the expression of human genes. Naturally carried by a small percentage of people, these mutations contribute to … Read More

Data parasites eh? - Code for life

Grant Jacobs Jan 24, 2016

Apparently researchers who use other’s data without collaborating with them are ‘research parasites’, according to an editorial from the New England Journal of Medicine. This has caused quite a fuss, with some expressing their opinion on the twitter streams #dataparasites and #researchparasites. I think the editorial conflates data sharing with other issues. Data sharing is an important part of science, but … Read More

What does a chromosome look like? (Not Just DNA #2) - Code for life

Grant Jacobs Nov 14, 2013

Aside from the fun of peering at the stuff that codes for the parts that make up us, knowing how a chromosome is arranged inside a cell nucleus might tell us a lot about how our genes work. Understanding the structures of genomes might well be what is needed to make sense of the genetics of complex diseases. Read More