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