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.
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.
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.
Kia ora! It is our great pleasure to invite you to the 17th GeneMappers Conference, to be held in Christchurch from Monday 19th to Wednesday 21st August. We are excited to host this meeting outside Australia for the first time, and aim to retain the ethos and build on the energy of previous meetings.
GeneMappers embraces all aspects of human genetics, genomics, and bioinformatics. It provides a forum for presentation and discussion of new research ideas and technologies, and is always a superb networking forum for scientists at all career stages.
The 2024 meeting will be held at the brand new Te Pae Convention Centre, in the heart of Christchurch city. We do hope you will take extra time to enjoy the city and its environs, and perhaps combine your visit with a winter break in the beautiful South Island (Te Waipounamu).
We look forward to welcoming you to Christchurch in August 2024!
Co-convenors
Martin Kennedy and Anna Pilbrow
University of Otago, Christchurch
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.
Metagenomics Summer School |
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