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Events

Upcoming events hosted by or involving Genetics Otago will be listed here. Please check back regularly for updates. A calendar of events that may be of interest to our members can be found at the bottom of this page and in the sidebar of other pages on this site, please note that this includes events hosted outside of Genetics Otago.

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VISG Seminar Series


The Virtual Institute of Statistical Genetics (VISG) Hub is a key part of Genetics Otago, providing a platform for researchers to collaborate and exchange knowledge and expertise in statistical genetics. The VISG Hub hosts seminars, workshops, and other events to promote statistical genetics research and foster collaboration between researchers.

We’re excited to announce our monthly genetics research seminars, aimed at connecting researchers in the field. The seminars will commence in May 2023 and will be hosted by GO’s Virtual Institute of Statistical Genetics (VISG) Hub along with the Department of Mathematics and Statistics at the University of Otago. These seminars will be available in person or via Zoom, and all are welcome.

Date: 3rd Thursday of the month
Time: 11:00 am – 12:00 pm

Schedule

  • May: Associate Professor Phil Wilcox, University of Otago
  • June: Professor Mik Black, University of Otago
  • July: Dr Ludovic Dutoit, University of Otago – please note that this seminar will be held on the 27th of July rather than the 20th due to ICG.
  • August: Dr Setegn Alemu, AgResearch
  • September: Ee Cheng Oi, Abacus Bio
  • October: Franziska Weik, Beef + Lamb NZ Genetics – Cancelled
  • November: Dr Jane Symonds and Dr Megan Scholtens, Cawthron – please note that this seminar will be held on the 17th of November rather than the 16th due to the Genetics Otago Annual Symposium.

Zoom Details
If you would like the Zoom details for this event, please contact us.

Next Seminar

The next seminar will be held on Friday the 17th of November, 11 am in Biochemistry Seminar Room G13 and will be given by Dr Jane Symonds and Dr Megan Scholtens, Cawthron Institute.

Title: Environmental resilience in aquatic species

Abstract: The New Zealand aquaculture sector faces growing vulnerability due to climate change, with marine heatwaves already causing elevated summer mortality rates in Greenshell mussels and king (Chinook) salmon. To tackle these challenges, selective breeding and genomic selection offer long-term solutions. Temperature challenge models, implemented in controlled tank environments, have been developed for both species. So far, this approach has been applied successfully to test more than 230 pedigree king salmon families and 21 Greenshell mussel families. Heritabilities for time to death at elevated temperature were high (0.34 to 0.48) suggesting that selection for improved thermotolerance is possible.

Megan Scholtens

Megan is a geneticist within the Aquaculture Group at Cawthron and is involved in a number of research projects across the ‘Shellfish Aquaculture’ and ‘Finfish Climate Change Adaptation’ platforms. Megan specialises in the application of genetic and genomic methodologies to enhance the understanding of how genes affect traits such as growth, development, behaviour, reproduction and immunity to improve the efficiency, resilience and survivability of aquatic species. In addition, Megan contributes to research activities of the Aquaculture team by integrating the experimental biology with commercial production to help provide solutions for clients and deliver tangible outcomes for the aquaculture industry.

Jane Symonds

Jane is a Senior Scientist and Team Leader in the Aquaculture Group at Cawthron. Jane’s focus is the application of research to enhance sustainable commercial production with a specific interest in king salmon farming and selective breeding. She has over 30 years of experience in this field. As a science programme leader she oversees a wide range of multi-disciplinary collaborative projects with internal and external partners, including salmon feed efficiency, genomics, behaviour, health, physiology, microbiomics, climate change adaptation, data science and developing trials to selectively breed resilient and efficient king salmon. Implementation of research for sustainable and profitable aquaculture development is a key driver for Jane. Dr Symonds is also a Senior Adjunct Researcher at the University of Tasmania and helps supervise multiple post-graduate students.

If you have any questions about this seminar series please contact us.

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Calendar of Events

The below is a calendar of events hosted by GO as well as events hosted by others that may be of interest to our members. If you have an event you would like us to include please contact us here.


Feb
7
Wed
eResearch NZ 2024 conference @ Intercontinental Wellington.
Feb 7 – Feb 9 all-day

7-9 February 2024 | Wellington
eResearch NZ is the leading conference for the research community in Aotearoa, New Zealand. Each year, it brings people together to connect, converse, and share their latest ideas and innovations.

In 2024, we’ll be hosting the event in Wellington. Our strategic theme is He Moana Pukepuke e Ekengia e te Waka | Navigating an evolving eResearch landscape

Together with the research community, we’ll be showcasing new innovations, technology and research while helping each other navigate the challenges in our changing field.

eResearch NZ is a collaborative initiative organised by REANNZ, NeSI and Genomics Aotearoa with the support of the wider community.

Feb
14
Wed
Genomics Aotearoa Training: Introduction to the Command Line @ Online
Feb 14 @ 10:00 am – 4:00 pm
Introduction to the Command Line
This online workshop will be taught on Wednesday 14th of February, 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.

Register for this workshop at Eventbrite.

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

Feb
28
Wed
Genomics Aotearoa Training: Introduction to R (online) @ Online
Feb 28 @ 10:00 am – 4:00 pm
Introduction to R (online)
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 28th of February, 2024. It 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.

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

Register for this workshop at Eventbrite.

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

Mar
6
Wed
Genomics Aotearoa Training: Long-Read Genome Assembly @ Online
Mar 6 @ 10:00 am – 4:00 pm
Long-Read Genome Assembly
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 6th of March, 2024. It is for New Zealand researchers interested in learning how to carry out genome assembly. This workshop will work through an entire assembly workflow, including data quality control, assembly, and assembly quality control.

This is an intermediate workshop, please check you meet the Prerequisites: Attendees must have introductory knowledge of Bash. We expect that you will either have completed our Introduction to bash workshop or have sufficient experience of your own.

Some of the topics covered in the workshop are:

  • Sequence data basics: HiFi and UltraLong read data specifics
  • Quality Control (QC) of the data: cleaning, read length filtering. Overview of phasing.
  • Assembly of a genome: Verkko and Hifiasm, comparison of the approaches.
  • Assembly QC: biological and technical assessments of the three Cs (contiguity, correctness, completeness).
  • Contiguity using gfastats
  • Correctness using Merqury
  • Completeness using asmgene
  • Assembly cleanup and genome annotation: checks for contamination, genome annotation using Liftoff, MashMap, and Minimap2.
  • Phased assemblies: the power of phased assemblies, with examples.

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.

Register for this workshop at Eventbrite.

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

Mar
20
Wed
Genomics Aotearoa TRAINING: RNA-seq Data Analysis @ Online
Mar 20 @ 10:00 am – 4:00 pm

RNA-seq Data Analysis

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on the Wednesday 20th of March, 2024. It is for New Zealand researchers interested in RNA-seq data analysis. The focus of this workshop is to analyse RNA-seq data with the aim to identify differentially expressed genes.

Some of the topics covered in the workshop are:

  • Quality assessment
  • Trimming and filtering
  • Mapping and read counts
  • Differential expression analysis
  • Over-representation analysis

Who this workshop is for:
This is a beginner-friendly workshop which assumes you are familiar with the basics of R ( e.g., you can copy basic functions like head, tail, or colSums, you are aware of how R stores files as Objects) and bash (e.g., can change directory with cd command, make a new folder with mkdir command, view contents using less command). If you would like a refresher on R you can find one here. If you would like a refresher on bash you can find one here.

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.

Register for this workshop at Eventbrite.

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

Mar
22
Fri
Genomics Aotearoa SEMINAR: Seeing evolution through a cladistic blindfold; the challenges of thinking about evolving lineages in a world of taxa @ Online
Mar 22 @ 10:00 am – 11:00 am

SEMINAR: Seeing evolution through a cladistic blindfold; the challenges of thinking about evolving lineages in a world of taxa

 

Tēnā koutou katoa
We are pleased to invite you to our first Genomics Aotearoa seminar for 2024, online on Friday, February 23 at 10am.

We welcome an international speaker to start the seminar series – Dr Ronald Jenner, who is Principal Researcher at the National History Museum in London. Ronald will be speaking to us live on “Seeing evolution through a cladistic blindfold; the challenges of thinking about evolving lineages in a world of taxa.”

Please note the 10am start time.   

We encourage you to 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 Ronald Jenner
Ronald is Principal Researcher at the Natural History Museum in London, UK. He researches the evolution of animal venoms and the conceptual history of phylogenetics. He is the author of Venom. The secrets of nature’s deadliest weapon (with Eivind Undheim) and Ancestors in evolutionary biology. Linear thinking about branching trees.”