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.
GO Annual Symposium
Genetics Otago has partnered with the Australasian Epigenetics Alliance to bring the AEpiA Conference to NZ for the first time, held 1st – 5th December 2024. The GO Symposium will begin with a shared session with the AEpiA delegates on the morning of the 5th of December and will then continue in its regular format for the remainder of the day.
As usual, the Symposium will highlight the fantastic research being done by GO members from around the country through presentations, posters and awards.
Date: Thursday 5th December 2024
Time: 9:00 am – 5:00 pm
Venue: Hutton Theatre, Otago Museum (for those joining from Christchurch and Wellington – a venue will be confirmed soon).
Programme
A draft programme will be available here soon.
Registration
Registration for this event is now open via the button below.
Abstract submission is part of the registration process, all abstracts must be submitted by no later than 5:00 pm on the 14th of November. Registration will close at 12:00 noon on Wednesday 20th November. Please keep the link provided at the end of your registration to make changes to your responses up until the closing date.
Registration Fee
Due to budget constraints, we will be charging a $50 per person registration fee for all attendees to subsidise the costs associated with the Symposium. We have received confirmation that this registration fee can be paid from S accounts, and if you are in a position to make a donation on top of this fee, we would gladly receive it. However, we do not want the payment to be a barrier to attendance, so if you are not in a position to make a payment, please contact us go@otago.ac.nz.
Payment Methods
Payments from an S account (or other University account) can be journaled to Genetics Otago account GL.10.LH.A14.2541 via your finance associate. Please include the surname(s) of the registrants that the payment covers in the narration.
If you need to make payment using funds from outside the University this can be arranged via the Cashier’s Office. Please contact us for details (go@otago.ac.nz).
Awards
The Annual Genetics Otago Awards including The Genetics Otago Award, Outstanding Mentor Awards, Student Supervisor Award, Publication Awards, Poster Awards and Science Communication Prize will be presented at the conclusion of the Symposium and nominations for these are now open.
Award nominations close at 12:00 noon on Wednesday 20th November (except for Poster and Science Communication Awards which are at 5 pm 14th of November) and should be submitted by email to go@otago.ac.nz.
Full details of the awards can be found here: Award Details.
Oxford Nanopore Technology Workshop
Join us at Ōtākou Whakaihu Waka, Dunedin, for a one day Oxford Nanopore Technology symposium. This event, jointly hosted by Genomics Aotearoa and the Genetics Otago ONT hub, will feature research talks highlighting different ONT use cases, a technical sequencing demonstration and an EPI2ME workshop.
This is an in-person event being held on Friday, December 6th at the Ōtākou Whakaihu Waka / University of Otago campus.
Registration for this event is free of charge.
This event is sponsored by ONT, and is supported by the Otago Genomics Facility.
Contact tyler.mcinnes@otago.ac.nz for any queries.
CRISPR Workshop
Details coming soon. Proposed date: 6th December.
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.
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.
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).
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 2nd of August, 2023, and is for New Zealand researchers interested in learning to write scripts and submit jobs to an HPC using a scheduler. This workshop is an excellent follow-up for everyone who has recently completed the Introduction to R and Introduction to Bash workshops, although these are not strictly prerequisites. You are expected to have some knowledge of basic terminal commands.
The following topics will be covered:
– Designing a variant calling workflow.
– Automating a workflow.
– An introduction to HPC.
– Working with job scheduler.
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.
Register for this workshop at Eventbrite here.
Training workshop: Intermediate Shell for Bioinformatics
Tuesday, July 18, 10am – 4pm, online
This workshop is hosted by Genomics Aotearoa and NeSI and is for New Zealand researchers interested in progressing their abilities with Shell.
The workshop will include:
An overview of the Shell, UNIX and Linux.
Downloading data from a remote source and checking data integrity.
Recap navigating files and directories, and commands used in routine tasks.
Inspecting and manipulating data, part 1 (the head, less, grep, and sed commands).
Inspecting and manipulating data, part 2 (using awk and bioawk to process text).
Automating file processing.
Challenges: solve example molecular biology problems using shell scripts.
This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:
Navigating files and directories.
An understanding of full versus relative paths.
Working with files and directories (examining files, creating, copying, moving and removing).
Use a command line-based text editor such as nano.
And have a basic understanding of:
File/directory permission in Linux.
For loops (preferred, not required).
If you lack the above skills, you can use these sites as a refresher: Introduction to Command Line Carpentries lesson https://datacarpentry.org/shell-genomics/
Setup: This is a fully online, 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 one week prior to the workshop.
You can view the workshop material, including the objectives and content, here: https://genomicsaotearoa.github.io/shell-for-bioinformatics/
Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.
Register for this workshop at Eventbrite
If you have any questions about this workshop, including whether it is suitable for you, please contact tyler.mcinnes@otago.ac.nz.
Join us from 24-26 July 2023 in either Auckland, Wellington or Dunedin for the PacBio HiFi Sequencing Experience Tour Roadshow Event. New Zealand is the ninth stop of the PacBio Asia Pacific HiFi Sequencing Experience Tour, to find out how HiFi sequencing is helping scientists find accurate and actionable genome-wide insights for the most important scientific discoveries.
Simply select one preferred location from the 3 locations in Auckland, Wellington, and Dunedin.
There will be presentations by industry-leading scientists and the opportunity for peer-to-peer discussions and networking during this event. Whether you have a single sample or a multi-genome project, complete and accurate long-read sequencing is designed to support your desire to make an impact.
Together with our partner, Millennium Science, we look forward to meeting you in person.
Highlights include:
The opportunity to connect with and hear from your peers
Immerse yourself in rich scientific content from across the Plant & Animal, Human, Rare & Inherited Diseases and Microbial genomics segments
Learn how to take full advantage of your samples and the PacBio HiFi advantage
See the website for more details.
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 26th of July, 2023, and is for New Zealand researchers interested in learning to create and work with pangenome graphs.
This workshop will include:
– An introduction to pangenome graphs.
– Setup guide for using the tools and data in the workshop.
– Overview of the PGGB toolkit.
– Choosing parameters to construct a graph.
– QC
– Extracting variant data.
– Mapping short reads against a pangenome graph.
This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:
– Navigating files and directories.
– An understanding on full versus relative paths.
– Working with files and directories (examining files, creating, copying, moving and removing).
– Use a command line-based text editor such as nano.
If you lack the above skills, you can use these sites as a refresher:
– Introduction to Command Line Carpentries lesson https://datacarpentry.org/shell-genomics/
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.
Register for this workshop at Eventbrite here.
Dovetail Genomics is organising a webinar with the title of “What is 3D genomics and why it matters”on 2nd Aug. In this webinar, we explore the vital role of chromosome folding and spatial organisation in gene regulation, and its seamless integration with multi-omic strategies such as transcriptomics and epigenomics. Discover real-world applications of 3D Genomics in gene regulation and oncology, including oncogenic regulation in multiple myeloma and enhancer hijacking in prostate cancer. Plus, learn how to effectively incorporate 3D Genomics into your research.
What you’ll learn:
- How 3D Genomics fits into the multi-omic toolbox (including ChIP-seq & ATAC-seq).
- What information 3D Genomics uniquely unlocks.
- Why integrating 3D Genomics provides valuable insight into your research.
Speaker: Cory Padilla, Ph. D., Product Manager, Dovetail Genomics, part of Cantata Bio
Department of Zoology Friday Seminar: 4th August, 12:00pm, Zoom
Invasive species, and the secrets they can teach us about the genetics of local adaptation.
Katarina Stuart (School of Biological Sciences, University of Auckland)
Invasive species present an invaluable opportunity to explore how organisms may cope with dramatic environmental shifts. Invasive species are introduced to new ranges, and must quickly respond to the new selection pressures in a process termed ‘rapid adaptation.’ At the same time, invasive species often undergo a genetic bottlenecking during translocation, which may cause a reduction of diversity in the population due to a loss of rare genetic variants. By studying the genetic shifts invasive populations have undergone, we may begin to understand better how genetic diversity supports a population’s ability to survive. In particular, ongoing developments in sequencing and analytical tools are enabling more comprehensive characterization of diverse components of genetic diversity present in natural populations. Here, we examine the invasion story of a well known avian pest, the common myna (Acridotheres tristis). Using whole genome resequencing we explore the impacts of successive bottlenecks on genomics variation, comparing patterns across a diverse range of different genetic variants, which include single nucleotide polymorphisms, structural variants, and transposable elements. With such data, we hope to better understand how components of genetic variation contribute to adaptive potential in an invasive population, as this has important implications not just in invasive species management and forecasting, but also in conservation efforts focused on vulnerable and managed native species.
Friday 4th August, 12:00pm
In-person hub: Benham seminar room (B215)
Zoom link: https://otago.zoom.us/j/97890882533?pwd=R0l0SXowNy9nTE02T21RZWUybjVoQT09
Meeting ID: 978 9088 2533
Password: 798823
Species-wide genomics of kākāpō provides transformational tools to accelerate recovery
A reminder about our Genomics Aotearoa seminar, online this Friday, August 4 at 3pm.
We welcome Dr Joseph Guhlin (University of Otago) to talk about Species-wide genomics of kākāpō provides transformational tools to accelerate recovery.
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 Joseph
Dr Joseph Guhlin graduated with a PhD in Plant & Microbial Sciences from the University of Minnesota.
Based at the University of Otago, he is working in the Genomics Aotearoa High Quality Genomes and Population Genomics programme. A programmer by trade, he is interested in small pop genomics, high-performance computing, gene family expansion and contractions, and applying machine learning to small populations and genetics.
