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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.


Apr
16
Tue
Genomics Aotearoa Training: Intermediate Shell for Bioinformatics @ Online
Apr 16 @ 10:00 am – 4:00 pm

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.

Apr
18
Thu
Ask The Experts: Hi-C Demystified, How to Choose the Right Assay for Your Project @ Online
Apr 18 @ 2:00 pm – 3:00 pm

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.

Apr
19
Fri
Introduction to Flow Cytometry Webinar @ Online
Apr 19 @ 9:00 am – 10:00 am
The Otago Micro and Nanoscale Imaging – Flow Cytometry Unit, in conjunction with Mediray and BioLegend, invites you to an Introduction to Flow Cytometry Webinar. This webinar will be in two parts and cover the following:
  • Introduction to spectral and traditional flow cytometry and data analysis (Session 1)
  • Considerations for Spectral Flow Cytometry Sample Preparation (Session 1/2)
  • Designing and optimising a multi-colour panel (Session 2)
Webinar time: 9:00 am to 10:00 am
Webinar dates are:
Note! Calendar links have been updated to include Microsoft Teams Meeting ID and Password as well.
Meeting ID: 215 871 135 447
Passcode: tPgUCh
Meeting ID: 435 413 551 830
Passcode: 6sA2Np
May
1
Wed
Genomics Aotearoa Early Career Researcher meeting @ Wellington
May 1 @ 8:00 am – May 2 @ 5:00 pm

Genomics Aotearoa is again holding its annual meeting of postdocs and early career researchers, organised by Training Coordinator Tyler McInnes. This year’s meeting in Wellington on May1-2 spans two days and includes a diverse spread of workshops and networking events.

 

More details to come.

 

May
8
Wed
Genomics Aotearoa: Single-Cell RNA-seq Analysis Workshop @ Online
May 8 @ 9:00 am – 1:00 pm

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8th, 9th, 15th and 16th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29th

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

  • Alignment and feature counting with Cell Ranger (briefly).
  • QC and exploratory analysis.
  • Normalisation.
  • Sctransform: Variant Stabilising transformation.
  • Feature selection and dimensionality reduction.
  • Batch correction and data set integration.
  • Clustering.
  • Identification of cluster marker genes.
  • Differential gene expression analysis.
  • Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

May
9
Thu
Genomics Aotearoa: Single-Cell RNA-seq Analysis Workshop @ Online
May 9 @ 9:00 am – 1:00 pm

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8th, 9th, 15th and 16th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29th

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

  • Alignment and feature counting with Cell Ranger (briefly).
  • QC and exploratory analysis.
  • Normalisation.
  • Sctransform: Variant Stabilising transformation.
  • Feature selection and dimensionality reduction.
  • Batch correction and data set integration.
  • Clustering.
  • Identification of cluster marker genes.
  • Differential gene expression analysis.
  • Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

May
15
Wed
Genomics Aotearoa: Single-Cell RNA-seq Analysis Workshop @ Online
May 15 @ 9:00 am – 1:00 pm

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8th, 9th, 15th and 16th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29th

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

  • Alignment and feature counting with Cell Ranger (briefly).
  • QC and exploratory analysis.
  • Normalisation.
  • Sctransform: Variant Stabilising transformation.
  • Feature selection and dimensionality reduction.
  • Batch correction and data set integration.
  • Clustering.
  • Identification of cluster marker genes.
  • Differential gene expression analysis.
  • Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

May
16
Thu
Genomics Aotearoa: Single-Cell RNA-seq Analysis Workshop @ Online
May 16 @ 9:00 am – 1:00 pm

This workshop, taught by Professor Mik Black, will introduce skills and tools required for the analysis of single-cell RNA-seq data (scRNA-seq data) in R. The workshop will be taught online over four half-days, on May 8th, 9th, 15th and 16th  (9am – 1pm). You should attend all 4 sessions.

This is an advanced workshop which requires an intermediate level of R knowledge and experience. To participate in this workshop you must have either completed the Genomics Aotearoa Intermediate R workshop, or have an equivalent level of experience (e.g., be a semi-regular R user). Because of the complexity of this workshop we will not have the time or resources to solve coding errors. However, the focus of this workshop will be on the concepts and discussion of the statistical methodology rather than your ability to code quickly.

Because we expect a high level of interest in this workshop and we have limited spaces, we are inviting expressions of interest no later than Friday April 26th and will select a group of attendees based on needs and experience. We will endeavour to maximise the overall positive impact on research in Aotearoa and distribute this training as fairly as possible. You will be advised whether you are able to attend the training by end of day Monday April 29th

If we are not able to offer you a space in this training, you will be kept informed about future options for scRNA-seq training.

What will this workshop cover?

  • Alignment and feature counting with Cell Ranger (briefly).
  • QC and exploratory analysis.
  • Normalisation.
  • Sctransform: Variant Stabilising transformation.
  • Feature selection and dimensionality reduction.
  • Batch correction and data set integration.
  • Clustering.
  • Identification of cluster marker genes.
  • Differential gene expression analysis.
  • Differential abundance.

*Note that some of this material may be mentioned only briefly due to time constraints, in which case you will be pointed towards supplementary material for self-guided learning.

If you have any questions about this workshop, please contact Genomics Aotearoa Training Coordinator Dr Tyler McInnes (tyler.mcinnes@otago.ac.nz).

Aug
19
Mon
Genemappers 2024 @ Te Pae Convention Centre
Aug 19 – Aug 21 all-day

Kia ora! It is our great pleasure to invite you to the 17th GeneMappers Conference, to be held in Christchurch from Monday 19th to Wednesday 21st August. We are excited to host this meeting outside Australia for the first time, and aim to retain the ethos and build on the energy of previous meetings.

GeneMappers embraces all aspects of human genetics, genomics, and bioinformatics. It provides a forum for presentation and discussion of new research ideas and technologies, and is always a superb networking forum for scientists at all career stages.

The 2024 meeting will be held at the brand new Te Pae Convention Centre, in the heart of Christchurch city. We do hope you will take extra time to enjoy the city and its environs, and perhaps combine your visit with a winter break in the beautiful South Island (Te Waipounamu).

We look forward to welcoming you to Christchurch in August 2024!

Co-convenors

Martin Kennedy and Anna Pilbrow
University of Otago, Christchurch