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.

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.

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.

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

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.

• 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)

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

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.

• 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)

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 8^th, 9^th, 15^th and 16^th  (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 26^th 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 29^th. 

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).