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
- August: Dr Setegn Alemu, AgResearch
- September: Ee Cheng Oi, Abacus Bio
- October: Franziska Weik, Beef + Lamb NZ Genetics
- November: Dr Jane Symonds and Dr Megan Scholtens, Cawthron
Zoom Details
If you would like the Zoom details for this event, please contact us.
June Seminar
The seminar will be held on the 15th of June in BI.G13, Biochemistry Building and will be given by Professor Mik Black of the Department of Biochemistry, University of Otago.
Title: Help! My genome turned into a graph…
Abstract: The recent release of a “draft human pangenome reference” has been hailed as providing access to a “more diverse human genome”. The incorporation of additional genetic diversity into what was previously a very non-diverse human reference genome was achieved through the use of “genome graph” methodology. Available in various forms for around five years now, methods for constructing genome graphs provide the ability to store both genomic sequence and genetic variation for any organism in a single graph-based representation of a genome, with additional genetic diversity (e.g., single-nucleotide variants (SNVs) and structural variants (SVs)) able to be added to an existing graph. This graph-based approach provides some major advantages over traditional linear reference approaches, however there are also a number of challenges that must be overcome for this methodology to become widely accepted. In this talk I will provide an overview of the current “linear reference” approach to genomic analysis, contrasting this with the additional opportunities offered by graph-based methodology. I will also present the results of work undertaken within the Genome Graphs project that has been funded by Genomics Aotearoa, where a graph-based approach has been applied in the area of pathogen genomics.
Biography: Professor Black is a member of the Centre for Translational Cancer Research, and his research focuses on the development of methods for the analysis of genomic data, with a strong emphasis on cancer and other human diseases. A common theme is the use of techniques that allow high-dimensional and often very disparate data sets to be combined in ways that provide new insights into disease development and progression:
Centre for Translational Cancer Research
This research is highly collaborative, and Mik works closely with a number of Otago research groups, as well as with long-standing national and international collaborators at the University of Auckland, the Institute of Environmental Science and Research, Wake Forest University Medical School, and Moffitt Cancer Center.
In addition to his own work, Mik has been heavily involved in establishing national research infrastructure in high performance computing through the NZ eScience Infrastructure, and in genomics and bioinformatics through Genomics Aotearoa, where he is the Chair of the Bioinformatics Leadership Team:
NZ eScience Infrastructure
Genomics Aotearoa
If you have any questions about this seminar series please contact us.
Please note the change in time and venue for this seminar due to the Stop Work meeting being held from 12 – 2 pm on the 9th of May.
It’s a team game: a research journey in infection and immunity
About Professor James Ussher’s research
James is an immunologist and a clinical microbiologist (at Southern Community Laboratories) whose research programme is focussed on the immune response to infection and on antibiotic resistance.
His laboratory is investigating the role of innate-like T-cells in anti-bacterial immunity and how they might be harnessed to prevent infection. They also contribute to several vaccine development projects. In addition, his laboratory uses whole genome sequencing of antibiotic resistant bacteria to identify outbreaks and track transmission pathways to enable interventions.
He is involved in collaborative research projects in New Zealand, the Pacific, Asia, and the United Kingdom.
In response to the COVID-19 pandemic, he co-led the establishment of the Vaccine Alliance Aotearoa New Zealand – Ohu Kaupare Huaketo (VAANZ), a multi-institutional team of researchers and industry focused on building New Zealand’s capability and platforms for vaccine development. He was a member of the Government’s COVID-19 Vaccine Taskforce and is a member of the COVID-19 Vaccine Technical Advisory Group.
Streaming information for Professor James Ussher
This event will be live-streamed, from 5:25pm Thursday 25th May 2023, at the following web address:
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on the Thursday 15th of June, 2023. 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: https://genomicsaotearoa.github.io/RNA-seq-workshop/
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.
Welcome to ResBaz Aotearoa 2023
40+ free and online digital research skills sessions
Designed for postgraduate students, researchers and those that support them in any discipline – all of the Aotearoa NZ research community
Register for taster and hands-on sessions across a week-long schedule
Look out for local meetups in your institution
Read more about ResBaz
Sessions are free but you must register your attendance via the sessions or schedule lists.
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.
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.
This in-person workshop is delivered by Genomics Aotearoa and NeSI, and will be taught over two consecutive days on 9-10 August 2023 from 10am-4pm NZT. It is for New Zealand researchers interested in signals of selection in genomes.
Sign up to this workshop at Eventbrite.
The focus of this workshop is on identifying signals of selection in an example genome using the outlier analysis method. Outlier analysis assumes that the majority of the genome is under neutral selection and some loci will appear as outliers relative to this background.
This lesson assumes learner has no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of selection. You are expected to have some familiarity with both the R programming language and with basic command line (bash). If you need to refresh, please revise the material in our previous workshops on R and bash.
We encourage you to bring your own data! For participants who do not have their own data, a group dataset is available and will be used by the instructors during the examples.
During this workshop you will:
Download example genomic data (or prepare your own).
Use the PCAdapt tool to identify outlier loci within a genome.
Use VCFtools to identify outlier SNPS in population comparisons.
Use Bayescan to identify outlier SNPS based on allele frequencies.
Relate identified SNPS to phenotypic variation.
Compare the results of the different methods and discuss the results.
Setup
This is an in-person, 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.
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.
Tyler McInnes
Training Coordinator, Genomics Aotearoa
www.genomics-aotearoa.org.nz
