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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.


Jun
1
Thu
eDNA Hub Seminar – Dr Quentin Mauvisseau @ D'Ath Lecture Theatre, Hercus Building
Jun 1 @ 1:00 pm – 2:00 pm

Jun
15
Thu
RNA-seq data analysis workshop @ Online
Jun 15 @ 10:00 am – 4:00 pm

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on the Thursday 15th of June, 2023. 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: https://genomicsaotearoa.github.io/RNA-seq-workshop/

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.

VISG Seminar Series @ Biochemistry Seminar Room G13
Jun 15 @ 11:00 am – 12:00 pm
Jun
20
Tue
ANCIENT DNA – FRIENDS IN FOCUS @ Barclay Theatre
Jun 20 @ 12:00 pm – 1:00 pm

Friends in Focus
Dr Nic Rawlence is the Director of the University of Otago’s Paleogenetics Laboratory. He spends his days excavating fossil sites and examining specimens in museum basements, all the while methodically analysing, researching and teaching on Aotearoa’s biggest and tiniest taoka.

With a research background in ancient DNA, the evolution of New Zealand’s extinct biodiversity, and the impacts climate change and humans have had on this prehistoric ecosystem, Dr Rawlence has plenty of insight into a world lost to time.

In this month’s edition of the Friends in Focus talk series, he will dive into what the latest discoveries using ancient DNA can tell us about the evolution of New Zealand’s taoka species and their future in a fast changing world.

Come along and hear from a leading New Zealand expert on this fascinating subject.

12.10pm, Tuesday 20 June
Barclay Theatre
Free – Koha Appreciated

Jun
26
Mon
ResBaz 2023 @ Online
Jun 26 – Jun 30 all-day

Welcome to ResBaz Aotearoa 2023
40+ free and online digital research skills sessions
Designed for postgraduate students, researchers and those that support them in any discipline – all of the Aotearoa NZ research community
Register for taster and hands-on sessions across a week-long schedule
Look out for local meetups in your institution
Read more about ResBaz

Sessions are free but you must register your attendance via the sessions or schedule lists.

Jul
4
Tue
eResearch @ Otago Day @ Room 117 Commerce Building
Jul 4 @ 9:30 am – 3:00 pm

eResearch @ Otago Day
Tuesday 4 July, 9:30am–3:00pm

This eResearch-focused event is free for all University staff and postgraduate students. This year’s event will be held in Room 117 of the Commerce Building (Zoom link available) and will focus on research being undertaken at the University as well as an update on new/upcoming eResearch services:
Short presentations by University of Otago researchers, specialist support staff, and some of our Research IT partner organisations, who are using electronic tools to help solve a variety of research and data management challenges.
Network with University of Otago researchers, specialist support staff, and staff from some of our Research IT partner organisations (REANZ and NeSI).
Learn about some of the IT services available to Otago researchers ranging from: mid-tier compute, HPC on NeSI; the REANNZ network; High Capacity Storage (HCS); the data transfer service and Library data management services.
You are welcome to forward this invitation to colleagues and postgraduate students.

When and Where:
Tuesday 4 July, 9:30am–3:00pm
Room 117 Commerce Building
Zoom: https://otago.zoom.us/j/95977317038?pwd=RHJJbS9BZDQ1ZkI4Y3hkV3N1cEY1Zz09
Meeting ID: 959 7731 7038
Password: 827288

RSVP:
If you’re joining us in person, we’ll start the day with morning tea and a light lunch will also be provided.
Please use the following link to RSVP by 9am on Tuesday 20 June so we can cater for you (https://forms.office.com/r/cZBErnEiya). This is a hard deadline for catering.

If you will be joining us via Zoom only – please still register so we can let you know about any updates and future eResearch events.

If you’re unable to join us on the day, but would like a link to the recorded talks, please email Nicola Walmsley (nicola.walmsley@otago.ac.nz). These will be available for a week after the event.

Questions:
If you have any queries about the event please contact Darren Hart (Manager, Research and Teaching IT Support, darren.hart@otago.ac.nz).

Advanced workshop: human genome assembly using long-read sequencing platforms @ University of Otago Dunedin Campus
Jul 4 @ 1:00 pm – Jul 6 @ 5:00 pm

Advanced workshop: human genome assembly using long-read sequencing platforms

Genomics Aotearoa, in collaboration with New Zealand eScience Infrastructure, is piloting an advanced workshop on human genome assembly using long-read sequencing platforms. This is an in-person workshop hosted at the University of Otago, starting in the afternoon of 4 July and ending in the afternoon of 6 July, 2023.

This workshop will be led by members of the Human Pangenome Reference Consortium (HPRC): Ann McCartney (Assistant Researcher, UCSC Genomics Institute) and Julian Lucas (Senior Bioinformatics Systems Analyst, UCSC Genomics Institute). The workshop’s main focus covers read handling, assembly generation, evaluation and curation. The workshop’s scope also includes comparisons between sequence platforms and popular long-read assemblers, examples of good and bad assemblies, and approaches to assembly phasing.

We are seeking your input, to ensure that this workshop is relevant to your research interests and analysis needs. We would like to hear your thoughts on how this workshop could benefit you and what content you would like to see included.

Please complete an expression of interest here to sign up to this workshop, and to share your experiences, feedback and suggestions.

Contact Jian Sheng Boey for further information.

 

Jul
6
Thu
VISG July Seminar: Dr Ludovic Dutoit
Jul 6 @ 2:10 am – 3:10 am

The seminar will be held on the 27th of July (note date change), 11 am in St David Seminar Room A and will be given by Dr Ludovic Dutoit of the Department of Zoology, University of Otago.

Title: Sex-linked stories in a shared genome
Abstract: When it comes to the genomics of sex, sex chromosomes are drawing most of the attention. While fascinating, they appeared much later than the sex phenotype itself. In this talk, I will explore the implications of a (mostly) shared genome on the evolution of sex. Using a combination of empirical and theoretical approaches, I will explore our current understanding of sexual conflict.

Biography: Ludo Dutoit has a range of research interests within evolutionary genomics. He is using population genomics, eDNA and transcriptomics tools to approach research questions in Ecology and Evolution. He has specific interests in understanding genomic signatures of sexual conflict, the speciation process and the evolutionary forces shaping genomic variation both in a fundamental context and within the realm of conservation biology.

Jul
7
Fri
Imputation workshop at LIC Hamilton @ TBA
Jul 7 @ 9:00 am – 5:00 pm

This in-person workshop is jointly hosted by LIC, Genomics Aotearoa and NeSI. It is for New Zealand scientists and will explore genotype imputation techniques.  Genotype imputation is a cost-efficient approach to approximate high-density genotypes or full sequence data from low-density genotypes/low-pass sequencing data of individuals. This workshop is intended for anyone interested in learning how to use either Beagle or Minimac to impute genotypes and how to evaluate the imputation performance of these methods.

This workshop will involve:

  • A brief overview of imputation.
  • Quality control and preparation of genetic data for imputation.
  • Evaluation the imputation performance using different parameters.
  • Workshop attendees will observe demonstrations and then work through exercises.

Prerequisites: Attendees are expected to have some familiarity with basic bash and R. If you would like a refresher, you can find a copy of past workshops which cover the fundamentals of bash (here) and R (here). Additionally, to get the most out of this workshop attendees are encouraged to know about basic genetics and genomics.

Setup: This is a hands-on workshop. The 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.

Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.

Sign up to the workshop at Eventbrite.

Jul
10
Mon
Ira Rangahau 2023 @ Terrace Lounge
Jul 10 @ 9:00 am – 5:00 pm

Genetics Otago together with Allan Wilson @ Otago is pleased to bring you the third Ira Rangahau Māori Symposium in July 2023. The inaugural Ira Rangahau took place in 2018, spearheaded by Associate Professor Phillip Wilcox (Ngāti Rakaipaaka, Rongomaiwahine, Ngāti Kahungunu ki te Wairoa). Since then, it has become a significant fixture in the Genetics Otago calendar. Building upon its success, the Ira Rangahau 2021 symposium saw the inclusion of Dr. Alana Alexander (Ngāpuhi: Te Hikutu, Pākehā) and Dr. Catherine Collins (Kāi Tahu, Pākehā) on the organising committee. This event expanded its reach by adopting a hybrid format, accommodating both in-person and online participation.

The 3rd Ira Rangahau Symposium will be held over a full day on the 10th of July 2023 on the Dunedin campus. This event will once again convene Māori kairangahau (researchers) from around the motu to present their genetics-related research spanning diverse domains from the primary sector to health, to whakapapa and te taiao (the environment). We also welcome another researcher to our organising committee, Dr Nathan Kenny (Te Ātiawa, Ngāi Tahu).