Training and Events

Overview

Presenter – Grace Hall

Most modern bioinformatic analyses are not possible without high-quality reference genomes. They are the backbone that supports current and future discoveries, and our collection of complete genome sequences are one of humanity’s greatest achievements.

Performing de novo assembly is easier than ever thanks to advances in long read sequencing and platforms such as Galaxy which enable bioinformatics workflows for non-coders. In this tutorial we will use the web-based analysis platform “Galaxy” to create a high-quality assembly of a Bacillus Subtilis strain. The software tools “Flye” and then “Pilon” will be used to perform the assembly and subsequent error correction to improve the accuracy of assembled contigs. You will learn how to will visualize input read sets and the assemblies produced at each stage and assess the quality of the final assembly.

Tools used

Galaxy, Flye, Pilon

Learning objectives

By the end of this training, participants will:

• understand how Nanopore and Illumina reads can be used together to produce a high quality genome assembly
• be familiar with genome assembly and polishing programs
• be able to perform de novo assembly using Nanopore and Illumina reads!

Prerequisites and Requirements

This workshop does not require any previous experience with working with sequencing reads, but familiarity with Galaxy and Galaxy workflows, or completion of “Introduction to Galaxy” workshop is required.

This is a hands-on workshop and attendees must bring their own laptops to the online workshop with the following software preinstalled:

• access to internet
• web browser (Firefox or Chrome recommended)
• Zoom (Version 5.1 or higher)

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes. For details of charges for external participants please see the Melbourne Bioinformatics Training page.

Overview

Presenter: Vicky Perreau

This detailed, hands on tutorial on Genome Browsers will provide beginners with an introduction to both the UCSC Genome browser and IGV (Integrated Genome Viewer). Numerous different datatypes will be displayed in the UCSC browser including human RNAseq data from GTEX and mouse single cell RNAseq data from Tabula Muris. Different data types available will be used to illustrate how a wide variety of biological questions can be investigated in genome browsers using public and local data.

Learning objectives

At the end of the workshop, you will be able to:

• find models for genes and transcripts of interest and interpret differences in the gene models
• find disease associated variants in the human genome
• determine the tissue/cell type expression profiles of a gene of interest and identify transcript variants expressed in different cell types
• understand some basic files types used in Genome browsers and upload and view local BAM files in genome browsers
• create custom interactive views with multiple datatypes to share with colleagues.

Prerequisites and Requirements

The workshop is aimed at bench researchers with no coding/programming skills who wish to learn how to utilise online data and resources to refine their biological research questions and discovery.

This is a hands-on workshop delivered via Zoom and attendees must use their own computers with the following software preinstalled:

• web browser (Firefox or Chrome recommended)
• IGV (Integrated Genome Viewer) (free)
• a computer mouse is also handy for selecting screen elements during the workshop.
• obtain a login to UCSC Genome browser (free) prior to the workshop to save your own sessions.
• Zoom (Version 5.1 or higher)

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes.

Overview

This workshop has been developed collaboratively by training specialists at Peter MacCallum Cancer Center and Melbourne Bioinformatics. It will be presented by Maria Doyle (Application and Training Specialist, Peter Mac) and Jessica Chung (Melbourne Bioinformatics, University of Melbourne). 

This introduction to R and RStudio will provide beginners with experience with loading, manipulating and visualising biological data using the tidyverse collection of R packages. The example data used is publicly available RNA-seq data, therefore attendees will gain experience in the structure and appearance of RNA-seq data.

Learning objectives

At the end of the course, you will be able to:

•    load tabular data into R

•    apply tidyverse functions to manipulate data in R

•    produce simple plots such boxplots using ggplot

•    understand and apply data faceting in ggplot

•    modify the aesthetics of a ggplot plot.

Prerequisites

The workshop is aimed at bench biologists with no coding/programming skills.

Attendees must use their own computer with RStudio and R installed (installation instructions available at this link). You may need to contact your own IT support for assistance during the installation process and to ensure that you have full permissions to R directories. Therefore, we advise you to begin installation when registering for the workshop, to allow sufficient time to troubleshoot issues with your own IT support such as permissions and sufficient space for installation. 

You will need:

• a charged laptop
• Web browser (Firefox or Chrome recommended)
• R (>= version 3.5) and RStudio installed on your laptop
• Zoom (Version 5.1 or higher)

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes.

Feedback, 2019

Overview

This workshop has been developed collaboratively by training specialists at Peter MacCallum Cancer Center and Melbourne Bioinformatics. It will be presented by Maria Doyle (Application and Training Specialist, Peter Mac) and Jessica Chung (Melbourne Bioinformatics, University of Melbourne). 

This introduction to R and RStudio will provide beginners with experience with loading, manipulating and visualising biological data using the tidyverse collection of R packages. The example data used is publicly available RNA-seq data, therefore attendees will gain experience in the structure and appearance of RNA-seq data.

Learning objectives

At the end of the course, you will be able to:

•    load tabular data into R

•    apply tidyverse functions to manipulate data in R

•    produce simple plots such boxplots using ggplot

•    understand and apply data faceting in ggplot

•    modify the aesthetics of a ggplot plot.

Prerequisites

The workshop is aimed at bench biologists with no coding/programming skills.

Attendees must use their own computer with RStudio and R installed (installation instructions available at this link). You may need to contact your own IT support for assistance during the installation process and to ensure that you have full permissions to R directories. Therefore, we advise you to begin installation when registering for the workshop, to allow sufficient time to troubleshoot issues with your own IT support such as permissions and sufficient space for installation. 

You will need:

• a charged laptop
• Web browser (Firefox or Chrome recommended)
• R (>= version 3.5) and RStudio installed on your laptop
• Zoom (Version 5.1 or higher)

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes.

Feedback, 2019

Overview

Presenter: Vicky Perreau

This detailed, hands on tutorial on Genome Browsers will provide beginners with an introduction to both the UCSC Genome browser and IGV (Integrated Genome Viewer). Numerous different datatypes will be displayed in the UCSC browser including human RNAseq data from GTEX and mouse single cell RNAseq data from Tabula Muris. Different data types available will be used to illustrate how a wide variety of biological questions can be investigated in genome browsers using public and local data.

Learning objectives

At the end of the workshop, you will be able to:

• find models for genes and transcripts of interest and interpret differences in the gene models
• find disease associated variants in the human genome
• determine the tissue/cell type expression profiles of a gene of interest and identify transcript variants expressed in different cell types
• understand some basic files types used in Genome browsers and upload and view local BAM files in genome browsers
• create custom interactive views with multiple datatypes to share with colleagues.

Prerequisites and Requirements

The workshop is aimed at bench researchers with no coding/programming skills who wish to learn how to utilise online data and resources to refine their biological research questions and discovery.

This is a hands-on workshop delivered via Zoom and attendees must use their own computers with the following software preinstalled:

• web browser (Firefox or Chrome recommended)
• IGV (Integrated Genome Viewer) (free)
• a computer mouse is also handy for selecting screen elements during the workshop.
• obtain a login to UCSC Genome browser (free) prior to the workshop to save your own sessions.
• Zoom (Version 5.1 or higher)

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes.