A reminder about this week’s Genomics Aotearoa seminar, online Friday, May 31 at 3pm.

We welcome Dafni Anastasiadi (Plant and Food Research). Dafni will be talking on Epigenetic clocks for age prediction.

Please invite colleagues to join our genomics community and take part in this seminar. Look forward to seeing you there. Questions and discussions are welcome.

Join from PC, Mac, iOS, or Android:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09

About Dafni
Dafni Anastasiadi is a scientist at Plant and Food Research, Nelson. Her research interests focus on the role of epigenetics in eco-evolutionary processes using marine species as models. Her work has produced results with far-reaching implications in the epigenetics field, including the first epigenetic clock to accurately predict age in fish.

WORKSHOP: Reproducible Bioinformatics with Nextflow and nf-core
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am to 4:00pm NZT on Wednesday the 5th of June, 2024, and is for New Zealand researchers interested in learning to use Nextflow.

Register for Reproducible Bioinformatics with Nextflow and nf-core

Nextflow is a management software system which facilitates the writing of scalable and reproducible scientific workflows. As a management system, Nextflow will simplify the development, monitoring, execution and sharing of pipelines. Using Nextflow will improve the reproducibility, portability, and run time of tasks.

Nextflow can integrate pipelines written in common scripting languages such as R and Python and couple these with environment management systems such as Docker, Singularity and Conda. Nextflow uses Domain Specific Language (DSL) which makes running workflows on cloud or high-performance computing (HPC) infrastructure easy.

This workshop will also introduce nf-core: a community-driven repository of peer-reviewed best practice analysis pipelines written in Nextflow.

This workshop is comprised of three sections:
Section 1
– An introduction to Nextflow.
– Useful terminology.
– Working in the Nextflow environment.
Section 2
– An introduction to nf-core – a repository of existing pipelines.
– General structure of a pipeline.
– Running and customising your first pipeline.
Section 3
– Customising and configuring pipelines.
– Metrics and shareable reports.

Setup
This is a fully online, hands-on workshop. This workshop material will be run on the NeSI OpenOnDemand training environment – there is no need to install any software for this workshop. Instructions on how to access the training platform will be sent out with the confirmation letter to registrants.
Participants must have their own laptops and plan to participate actively. You will require a working web browser.
Prerequisites: You must have basic command line (Bash) skills to participate in this workshop.
If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 17th of July, 2024, and is for New Zealand researchers interested in learning R. This workshop functions as a prerequisite for the RNA-seq Data Analysis workshop, and the material provides a basis for many workflows in R.

Some of the topics covered in the workshop are:

– An introduction to R and RStudio.

– R basics: The R language, reading data into R, storing data as objects.

– R packages.

– Publication-quality data presentation using ggplot2.

– Knitr: keep track of workflow and produce easy-to-follow reports of your work.

– Where to get more help when you are ready to do more.

We assume the learner has no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts.

Setup

This is a fully online, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

The material for this workshop can be previewed here:

https://genomicsaotearoa.github.io/Introduction-to-R/

Participants must have their own laptops and plan to participate actively. You will require a working web browser.

If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.

We are delighted to invite you the Genomics Aotearoa seminar series.

Professor Scott V. Edwards will be presenting a talk on Peering into the lives of the little bush moa (Anomalopteryx didiformis) and relatives through their genomes

Because of time zones, this seminar will be held earlier than usual.
Please join us on Friday, July 19th at 12pm (NZT).

Scott V. Edwards is Alexander Agassiz Professor of Zoology and Curator of Ornithology in the Museum of Comparative Zoology and is currently Chair of the Department of Organismic and Evolutionary Biology at Harvard University. Scott is an evolutionary biologist, with diverse interests in molecular evolution, phylogenetics, comparative genomics and population genetics. His research uses birds as model systems, focusing on their evolutionary history, phylogeography and genome evolution. His current work focuses on using phylogenetic trees and statistical models to link genomic and phenotypic variation. Scott has served as President of the Society for the Study of Evolution, and the Society of Systematic Biologists, and has served on the Advisory Boards of the National Museum of Natural History (Smithsonian) and the Cornell Lab of Ornithology. In 2015 he gave a multi-city lecture tour of Aotearoa, New Zealand, focusing on the imprints of dinosaur ancestry on the genomes of modern birds. From 2013-2015 Scott served as Division Director of the Division of Biological Infrastructure at the US National Science Foundation, where he facilitated funding in areas such as undergraduate research experiences, supporting biological collections and major infrastructure and bioinformatics. He also has led efforts to increase the diversity of undergraduates in evolutionary biology and biodiversity science.

Questions and discussions are welcome. We encourage you to invite colleagues to join our genomics community and take part in this seminar. Look forward to seeing you there.

Join from PC, Mac, iOS, or Android:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 24th of July, 2024, and is for New Zealand researchers interested in advancing their skills with R.

This is an intermediate workshop, please check you meet the Prerequisites: Attendees must have introductory knowledge of R and be well versed in tidyverse (Intro to R + supplementary materials in that workshop). We expect that you will either have completed our Introduction to R workshop or have sufficient experience of your own.

Some of the topics covered in the workshop are:

– Introduction to relational data and the join function.

– Working with regular expressions and functions from the stringr package.

– Writing custom functions, working with conditional statements.

– ‘Defensive programming’.

– Iterations – for loops, and map_*() functions.

– The importance of data structure in R.

Setup

This is a fully online, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

The material for this workshop can be previewed here.

Participants must have their own laptops and plan to participate actively. You will require a working web browser.

If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.

This online workshop will be taught on Wednesday 31st of July, 2024 10:00am-4:00pm NZT and is for New Zealand researchers interested in learning to use the command line.

The focus of this workshop is on working with the command line, also called The Shell.

Some of the topics covered in this workshop are:

An introduction to the Shell, including why this is such a powerful tool.
File navigation, how to navigate directories.
How to interact with files – copy or rename files in bulk. Automation reduces user error and saves time.
Redirection: passing information from one command to another to create useful chains of commands.
Writing scripts which can be executed to quickly and easily reproduce analyses.
This lesson assumes learner has no prior experience with the tools covered in the workshop.

Setup

This is a fully online, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

The material for this workshop can be previewed here.

Participants must have their own laptops and plan to participate actively. You will require a working web browser.

If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.