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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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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.


Mar
20
Wed
Genomics Aotearoa TRAINING: RNA-seq Data Analysis @ Online
Mar 20 @ 10:00 am – 4:00 pm

RNA-seq Data Analysis

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on the Wednesday 20th of March, 2024. 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.
Participants must have their own laptops and plan to participate actively. 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.

Mar
22
Fri
Genomics Aotearoa Seminar Series: “Seeing evolution through a cladistic blindfold; the challenges of thinking about evolving lineages in a world of taxa.” @ Online
Mar 22 @ 10:00 am – 11:00 am

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.

Genomics Aotearoa SEMINAR: Seeing evolution through a cladistic blindfold; the challenges of thinking about evolving lineages in a world of taxa @ Online
Mar 22 @ 10:00 am – 11:00 am

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.”

Mar
27
Wed
Genomics Aotearoa Training: Introduction to Bash Scripting and HPC Job Scheduler Online @ Online
Mar 27 @ 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 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.

Asia-Pacific Genetics Seminar: Surveillance and countermeasures against coronaviruses with potential spillover from wildlife. @ Online
Mar 27 @ 4:00 pm – 5:00 pm

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.

Apr
5
Fri
Genomics Aotearoa Seminar: Should I trust my bioinformatic tools? @ Online
Apr 5 @ 3:00 pm – 4:00 pm

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

About Paul Gardner
Dr Paul Gardner is an Associate Professor in the Department of Biochemistry,  University of Otago, and has worked with Genomics Aotearoa on Identifying genetic drivers of Streptococcus pyogenes, and Medical Metagenomics.
He has devoted over two decades to research in bioinformatics, particularly in the application and development of machine learning techniques. His work has advanced our understanding of non-coding RNAs, genomic variation, and molecular evolutionary biology, among other areas.
Apr
10
Wed
Genomics Aotearoa Training: Intermediate R (online workshop) @ Online
Apr 10 @ 10:00 am – 4:00 pm

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.

Apr
11
Thu
Introduction to Flow Cytometry Webinar @ Online
Apr 11 @ 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
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.