eResearch @ Otago Day
Tuesday 4 July, 9:30am–3:00pm

This eResearch-focused event is free for all University staff and postgraduate students. This year’s event will be held in Room 117 of the Commerce Building (Zoom link available) and will focus on research being undertaken at the University as well as an update on new/upcoming eResearch services:
Short presentations by University of Otago researchers, specialist support staff, and some of our Research IT partner organisations, who are using electronic tools to help solve a variety of research and data management challenges.
Network with University of Otago researchers, specialist support staff, and staff from some of our Research IT partner organisations (REANZ and NeSI).
Learn about some of the IT services available to Otago researchers ranging from: mid-tier compute, HPC on NeSI; the REANNZ network; High Capacity Storage (HCS); the data transfer service and Library data management services.
You are welcome to forward this invitation to colleagues and postgraduate students.

When and Where:
Tuesday 4 July, 9:30am–3:00pm
Room 117 Commerce Building
Zoom: https://otago.zoom.us/j/95977317038?pwd=RHJJbS9BZDQ1ZkI4Y3hkV3N1cEY1Zz09
Meeting ID: 959 7731 7038
Password: 827288

RSVP:
If you’re joining us in person, we’ll start the day with morning tea and a light lunch will also be provided.
Please use the following link to RSVP by 9am on Tuesday 20 June so we can cater for you (https://forms.office.com/r/cZBErnEiya). This is a hard deadline for catering.

If you will be joining us via Zoom only – please still register so we can let you know about any updates and future eResearch events.

If you’re unable to join us on the day, but would like a link to the recorded talks, please email Nicola Walmsley (nicola.walmsley@otago.ac.nz). These will be available for a week after the event.

Questions:
If you have any queries about the event please contact Darren Hart (Manager, Research and Teaching IT Support, darren.hart@otago.ac.nz).

Advanced workshop: human genome assembly using long-read sequencing platforms

Genomics Aotearoa, in collaboration with New Zealand eScience Infrastructure, is piloting an advanced workshop on human genome assembly using long-read sequencing platforms. This is an in-person workshop hosted at the University of Otago, starting in the afternoon of 4 July and ending in the afternoon of 6 July, 2023.

This workshop will be led by members of the Human Pangenome Reference Consortium (HPRC): Ann McCartney (Assistant Researcher, UCSC Genomics Institute) and Julian Lucas (Senior Bioinformatics Systems Analyst, UCSC Genomics Institute). The workshop’s main focus covers read handling, assembly generation, evaluation and curation. The workshop’s scope also includes comparisons between sequence platforms and popular long-read assemblers, examples of good and bad assemblies, and approaches to assembly phasing.

We are seeking your input, to ensure that this workshop is relevant to your research interests and analysis needs. We would like to hear your thoughts on how this workshop could benefit you and what content you would like to see included.

Please complete an expression of interest here to sign up to this workshop, and to share your experiences, feedback and suggestions.

Contact Jian Sheng Boey for further information.

The seminar will be held on the 27th of July (note date change), 11 am in St David Seminar Room A and will be given by Dr Ludovic Dutoit of the Department of Zoology, University of Otago.

Title: Sex-linked stories in a shared genome
Abstract: When it comes to the genomics of sex, sex chromosomes are drawing most of the attention. While fascinating, they appeared much later than the sex phenotype itself. In this talk, I will explore the implications of a (mostly) shared genome on the evolution of sex. Using a combination of empirical and theoretical approaches, I will explore our current understanding of sexual conflict.

Biography: Ludo Dutoit has a range of research interests within evolutionary genomics. He is using population genomics, eDNA and transcriptomics tools to approach research questions in Ecology and Evolution. He has specific interests in understanding genomic signatures of sexual conflict, the speciation process and the evolutionary forces shaping genomic variation both in a fundamental context and within the realm of conservation biology.

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.

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.