This online workshop will be taught on Wednesday 31st of July, 2024 10:00am-4:00pm NZT and is for New Zealand researchers interested in learning to use the command line.

The focus of this workshop is on working with the command line, also called The Shell.

Some of the topics covered in this workshop are:

An introduction to the Shell, including why this is such a powerful tool.
File navigation, how to navigate directories.
How to interact with files – copy or rename files in bulk. Automation reduces user error and saves time.
Redirection: passing information from one command to another to create useful chains of commands.
Writing scripts which can be executed to quickly and easily reproduce analyses.
This lesson assumes learner has no prior experience with the tools covered in the workshop.

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.

We are delighted to invite you Genomics Aotearoa’s seminar, on Friday, August 2nd, 3-4pm.

Dr Karla Araya Castro will be presenting For Humans, Plants, and Genomics: Communication is the Key

Questions and discussions are welcome. We encourage you to invite colleagues to join our genomics community and take part in this seminar. Look forward to seeing you there.

Join from PC, Mac, iOS, or Android:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09

Karla Araya Castro is a biotechnologist with a Master’s and PhD in Natural Resources Science. She is currently a visiting postdoctoral researcher at the Department of Biochemistry in the School of Biomedical Sciences at the University of Otago. Her research focuses on nanotechnology applied to plants, specifically using lipid-based nanoparticles for the delivery of specific plant miRNAs.

In parallel with her scientific career, Karla has gained extensive experience in social entrepreneurship and product development across various industries.

In Chile, while completing her undergraduate degree at Universidad de La Frontera, Karla led projects that extended beyond her passion for science. In 2009, she applied to the Melton Foundation and became part of a large international network that actively promotes global citizenship as a way for individuals and organizations to collaborate across boundaries of place and identity to address global challenges. Through this network, Karla participated in various social and intercultural projects and had the opportunity to travel to Germany and China, where she not only gained invaluable knowledge and experience but also came to understand that disability is a matter of context rather than individual limitations.

In 2010, alongside her undergraduate studies, she completed a Diploma in Democratic Leadership. Upon graduating with a degree in Biotechnology, Karla was awarded the Faculty of Agricultural and Forestry Sciences Prize in recognition of her personal and academic qualities, and her special dedication to promoting the prestige of her career and faculty.

In 2014, she began her PhD studies, and during the same year, through her involvement with the Melton Foundation and the Climate Reality Project, she traveled to South Africa for training and mentoring in climate change at a conference led by Al Gore, former Vice President of the United States. In November of that same year, she traveled to Rio de Janeiro, where she served as a mentor for the development of new leaders in climate reality. In 2016, she represented the Melton Foundation in a D-Lab project, a Massachusetts Institute of Technology (MIT) program designed to connect innovators from around the world to work on low-cost, high-impact technologies for communities. As part of this initiative, Karla also traveled to Zambia and participated in a co-design summit, where she and the Kafue community in Lusaka developed simple solutions to address contaminated water issues.
In 2018, she participated in a program to tackle industry-based challenges, from which she led the initiative “PicaPellet: A Sustainable Alternative for the Production of Solid Biofuel from Ulex europaeus” for a fuel company. In the same year, she received funding to start “InclusivApp,” an initiative aimed at bridging the information gap regarding urban accessibility in the city of Temuco. Through this project, she was recognized as one of the 100 Women Leaders in the La Araucanía region in 2020.

During the long lockdown in Chile due to COVID-19, she was a lecturer for a course she designed called “Science in Quarantine” at PROENTA-UFRO, a program for children and youth with academic talents.
Karla describes herself as a resilient and somewhat stubborn woman, a mother to Amelia and Máximo, a person with a physical disability, a wheelchair user, and a wine lover.

This online workshop is hosted by Genomics Aotearoa and NeSI. The workshop will be taught from 10:00am-4:00pm NZT on the 7th of August 2024 and is for New Zealand researchers interested in progressing their abilities with Shell.

This workshop will cover:

– 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 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.

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 21st of August, 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.

Career Evening

Unsure what you can do with a Genetics, Biochemistry, Microbiology or Neuroscience background? Come along and hear about some avenues from local graduates and employers.

Who should attend? This event is open to all 300 and 400-level students in Genetics, Biochemistry, Neuroscience and Microbiology, as well as interested postgraduate students. The event has limited spaces, please RSVP by Wednesday 18th September to secure your place at this event.

What the event involves? The evening will begin at 6:00 pm with short presentations from the guest speakers, followed by an opportunity to chat and network with the speakers over pizza. Details of speakers will be published here once confirmed.

Date: 25th September 2024
Time: 6:00 pm – 8:00 pm
Location: BI.G13, Biochemistry Building

Career Evening Poster

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught over two mornings from 9:00am-1:00pm NZT on Tuesday 8th October and Wednesday 9th October, 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.

During Day 1 we will cover quality control and read cleaning, alignment and quantification methods, and carry out an exploratory analysis of an example data set.

During Day 2 we will work through two methods which take unique statistical approaches to identifying differentially expressed genes. We will then look at over-representation analysis, a popular method to derive biological meaning from a list of differentially expressed genes.

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.

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.

This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught over two mornings from 9:00am-1:00pm NZT on Tuesday 8th October and Wednesday 9th October, 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.

During Day 1 we will cover quality control and read cleaning, alignment and quantification methods, and carry out an exploratory analysis of an example data set.

During Day 2 we will work through two methods which take unique statistical approaches to identifying differentially expressed genes. We will then look at over-representation analysis, a popular method to derive biological meaning from a list of differentially expressed genes.

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.

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.

Genomics Aotearoa and NeSI are proud supporters of the Bioinformatics Spring School 2024, being organised by the University of Otago to run from Monday 18^th – Friday 22^nd November 2024.

Spring School is an intensive, one-week course tackling the basics of BASH (a command line language) and an introduction to the R programming language, working with Genomic DNA, RNA-seq data analysis, eDNA, and long-read genome assembly. During the workshops you will also be introduced to working on high performance computers and exposed to good bioinformatics practices.

This in person event is excellent experience for someone starting their bioinformatics journey and will provide a general introduction as well as touching on some of the common workflows used in genomic data analysis.

Expressions of interest applications close midnight Friday 29^th September.

To know more about the event visit Otago Bioinformatics Spring School 2024.

Submit your interest using this google form.

Contact Dr Murray Cadzow, University of Otago, for further information: murray.cadzow@otago.ac.nz