Workshops in NZ

Many Universities, Crown research institutions, and other groups coordinate and deliver valuable upskilling opportunities for NZ based researchers. This page, originally created by Genomics Aotearoa and New Zealand eScience Infrastructure, is for listing NZ-friendly digital skills workshops. We encourage anyone who is instructing at or coordinating a training event to post their workshop details on this page, even if it is a ‘closed’ or private event.

Page purpose: to raise awareness of NZ training events and encourage inter-institutional collaboration.

How to add a workshop to this page: Instructions coming soon

Upcoming Workshops

July 2021

Genomics Data Carpentry, 27-28 July, Online

Co-hosted by Genomics Aotearoa and NeSI, this online introductory workshop will help you get started with genomic data analysis. Specifically, attendees can expect to learn: Project organization and management - Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database. Introduction to the command line - Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards. Data wrangling and processing - Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation. Introduction to cloud computing and High Performance Computers (HPCs) for genomics - Learn how to work with NeSI HPCs and how to transfer data between your local computer and the HPC platform.

Prerequisites: This online workshop is for beginners to bioinformatics but basic genomics knowledge is expected. Learners should have some familiarity with biological concepts and must bring their own laptops. This is a hands-on workshop and participants are encouraged to participate actively.

Registration: To attend, you must register in advance. Instructions for connecting to the online session will be emailed to all registrants.

Register here: https://foreal17.github.io/2021-07-27-Online/

August 2021

Imputation Workshop, 11th August 2021 - LIC, Hamilton

Genotype imputation is a key component of modern genetic studies. It 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. A brief overview of imputation will be followed by demonstrations and exercises, including:

Dates TBA

mixOmics workshop for omics data integration, Palmerston North

There will be a mixOmics workshop at Massey University, Palmerston North. More details, including a tentative content, to be fine-tuned with the audience can be found at this link: http://mixomics.org/2021/05/june-28-30-2021-palmerston-north-nz-beginner/

Register your interest here: https://forms.gle/MgFdvVjRdtnPr92UA and lock in your dates in your diary! Survey closes on Tuesday 7 June with registration confirmation announced a day later. Partial or total registration fee waivers available to selected PhD student applicants.
Contact: Kim-Anh: kimanh.lecao@unimelb.edu.au or Matthieu: M.Vignes@massey.ac.nz

Past Workshops

Environmental DNA Workshop, 24-25 June 2021, Auckland

Advances in genomics over the past decade have greatly expanded the breadth of community ecology, and enabled fine scale study of many ecosystems. Environmental DNA (eDNA) is DNA material isolated from environmental substrates, including water, soil, air, or even within larger organisms (using a broader definition of ‘environment’). The eDNA samples can be amplified with PCR and sequenced with next-generation sequencing technologies to study the biodiversity of the environment, in a method called metabarcoding. In this workshop we will review the most common methods for metabarcoding in order to identify the taxonomic components and determine the relationship across these communities. Through a combination of demonstration and hands-on practicals, you will learn the basic concepts and core tools needed to analyse eDNA metabarcoding data for a wide range of studies.
Workshop_Link

NeSI know-how webinar 3: What to know about GPUs - Online (6 May)

Registrations: Click here to register
Contact: training@nesi.org.nz

RNA-seq workshop - Massey Univeristy, Palmerston North (18-19 May)

Registrations: Click here to register
Contact: ngoni.faya@otago.ac.nz

NeSI know-how webinar 1: 4 tips for getting started with NeSI - Online (15 April)

Registrations: Click here to register
Contact: training@nesi.org.nz

Globus update for IT professionals in NZ - Online (20 April)

Registrations: Click here to register
Contact: training@nesi.org.nz

Carpentries Community Discussion | All about HPC Carpentry - Online (21 April 3:00pm NZDT)

Registration: Sign up for the discussion here
Contact: megan.guidry@nesi.org.nz

NeSI know-how webinar 2: Using Jupyter on NeSI - Online (22 April)

Registrations: Click here to register
Contact: training@nesi.org.nz

Ecology Data Carpentry - Dunedin (7th -8th)

Workshop site: https://otagocarpentries.github.io/2021-04-07-otago/
Contact: murray.cadzow@otago.ac.nz

RNA-seq Workshop - Dunedin (9th)

Workshop: site
Contact: ngoni.faya@otago.ac.nz

Carpentries Community Discussion about teaching online - Online (31 March 3:00pm NZDT)

Registration: Sign up for the discussion here
Contact: megan.guidry@nesi.org.nz

Collaborative event | Machine Learning 101 on NeSI - Wellington (29 March All day)

Location: in-person Greta Point, Wellington Registrations: TBA
Contact: megan.guidry@nesi.org.nz

Massey Uni | Data Organization in Spreadsheets for Ecologists - Online (29 March 2-4pm NZDT)

Registrations: Closed
Contact: megan.guidry@nesi.org.nz

Hi-C Workshop - Auckland (25th - 26th March)

Workshop: site
Contact: ngoni.faya@otago.ac.nz

RMarkdown for Researchers: Weave together narrative text and code - Online (24th 12-1pm NZDT)

Click here to register
Contact: megan.guidry@nesi.org.nz

Genomics Data Carpentry - Online (16th - 17th March)

Workshop material