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.
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.
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.
On Friday March 22 at 10 am we present another international speaker – Ronald Jenner, Principal Researcher at the Natural History Museum in London. Ronald researches the evolution of animal venoms and the conceptual history of phylogenetics, and 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.”
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 let colleagues know, and note the 10am start time.
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.”
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 27th of March, 2024, 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.
Some of the topics covered in the workshop are:
– 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.
Tēnā koutou katoa
Please join us on Wednesday, March 27 at 4pm (NZDT) for the next seminar in the Asia-Pacific Genetics Seminar Series. Register in advance to receive an email with a link to the seminar.
Dr Shi Zhengli will be presenting on Surveillance and countermeasures against coronaviruses with potential spillover from wildlife.
Dr Shi is Professor Director of the Center for Emerging Infectious Diseases, Wuhan Institute of Virology (Chinese Academy of Sciences), and the Group Leader for the Emerging Virus Team.
| Dr Shi focuses her research on the pathogen investigation of unknown viruses in wild animals and the interspecies infection mechanism of zoonotic viruses. She is in charge of the viral surveillance screening of bat samples, leading to the discovery and recognition of a wide-array of new SARS-like coronaviruses, adenoviruses and adeno-associated viruses in mainland China.
Her experience with bat coronavirus led to the rapid identification of the pathogen COVID-19 and its probable bat origin. Dr Shi won the 2018 State Natural Science Award of China (Second Class), and was elected as a fellow of the American Academy of Microbiology in 2019. She has served since 2017 as Editor-in-Chief for Virologica Sinica. |
The Asia-Pacific Genetics Seminar Series
The Asia-Pacific Genetics Seminar Series is a collaboration between the Genetics Society of Japan (GSJ) and the Genetics Society of Australasia (GSA). The quarterly seminar aims to further develop the field of genetics and promote international exchange among researchers in Asia and the Pacific.
Tēnā koutou katoa
We are pleased to invite you to our Genomics Aotearoa seminar, online on Friday, April 5 at 3pm.
We welcome Dr Paul Gardner, Associate Professor in the Department of Biochemistry at the University of Otago. Paul will be talking on Should I trust my bioinformatic tools?
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
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Advance your skills with R! You will learn to complete R tasks with fewer lines of code, scale your analyses, and write readable code.
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 10th of April, 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.
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Introduction to spectral and traditional flow cytometry and data analysis (Session 1)
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Considerations for Spectral Flow Cytometry Sample Preparation (Session 1/2)
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Designing and optimising a multi-colour panel (Session 2)
Passcode: tPgUCh
This online workshop is hosted by Genomics Aotearoa and NeSI. The workshop will be taught from 10:00am-4:00pm NZT on the 16th of April 2024. It is for New Zealand researchers interested in progressing their abilities with Shell. The workshop will cover Shell overview, downloading and verifying data, inspecting and manipulating text data with Unix tools, automating file-processing.
This 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 bioawkto 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 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.
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.
You can view the workshop material, including the objectives and content here.
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 these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.
Webinar
Ask The Experts: Hi-C Demystified |
How to Choose the Right Assay for Your Project |
Speaker:
Dr. Myriam El Khawand leads the customer success team at Dovetail Genomics and has been with the company for over 5 years helping customers achieve their research goals using Dovetail proximity ligation kits and analysis solutions.
| What will be covered: |
| 3D genomics explores the influence that chromatin architecture plays in gene regulation. The primary method employed is Hi-C. With Hi-C coming in many flavors and forms, it can be overwhelming to know which assay is going to work best for your research goals.
Join us for this technical webinar where we will go into the ins and outs of the different Hi-C methods and chemistries, provide guidance on when to choose a particular option, and discuss the implications of that choice. Myriam’s presentation will include time for an in-depth QnA. |
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Introduction to spectral and traditional flow cytometry and data analysis (Session 1)
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Considerations for Spectral Flow Cytometry Sample Preparation (Session 1/2)
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Designing and optimising a multi-colour panel (Session 2)
Passcode: tPgUCh
