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.
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.
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)
-
Considerations for Spectral Flow Cytometry Sample Preparation (Session 1/2)
-
Designing and optimising a multi-colour panel (Session 2)
Passcode: tPgUCh
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.
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).
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).
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).