Workshops

The COMBINED ABACBS & Phylomania conference will be held in Sydney during the week starting 22nd - 26th November 2021. The workshops will run in parallel with the Phylomania conference. These workshops will be dedicated to workshops that are focused on specific technical areas of interest, often with a practical hands-on component. At past conferences, these have been extremely popular events, and many have sold out early. The Reactome pathways analysis workshops will be on the afternoon of Thursday, 25th November, while the Clinical Informatics workshop and the Metagenomics data analysis workshop will be on Friday, 26th November. For the workshops which involves hands-on tutorials, please bring your own laptop for working on the hands-on components.

Participants can register just for the workshop(s) without registering for the conference.

Questions on the workshops should be emailed to the contact person for each workshop.

Costs are the same for each workshop (as shown below):

There are three workshops:

  • Pathway analysis of multi-omics data using the Reactome database (Thursday, 26 Nov)

  • Clinical Bioinformatics Symposium (Friday, 27 Nov)

  • Viral Metagenomics with Hecatomb (Friday, 27 Nov)

Registrations

Workshops (members): $10 per workshop per person

Workshop (non-members): $15 per workshop per person

To REGISTER for the workshops please click here.

Thursday, 25 November

Pathway analysis of multi-omics data using the Reactome database 

Training Team: 

Ignatius Pang (main contact)  ipang@cmri.org.au

Nader Aryamanesh

Pablo Galaviz

The training team will consist of senior bioinformaticians from the Children’s Medical Research Institute, Westmead, Sydney.

Proposed number of attendees: 20 maximum

Start time:

  • AWST 11:15

  • AEST 13:15

  • ACST 13:45

  • AEDT 14:15

  • NZ 15:15

Run Time:  2 hours 45 mins

Workshop delivered virtually via Zoom with hands-on breakout sessions.

Abstract

Transcriptomics and proteomics experiments often produce lists of genes or proteins that show statistically significant differential expression when samples from different experimental conditions, genotypes, or tissue types were compared. To investigate whether significantly differentially expressed genes or proteins were overrepresented in specific biological pathways and provide insights on their functions, curated databases that map genes and proteins to biological pathways were often used. One such curated database is the Reactome (Jassal et al. 2020 NAR, 48(D1):2115-2125), which is a database of manually curated biological pathway maps (e.g. metabolic, signalling and regulatory pathways). The Reactome analysis engine also enables quantitative -omics data as input, using tools such as CAMERA (Wu and Smyth 2012 Mol. Cell Proteomics, 19(12):e133) and PADOG (Tarca et al. 2012 BMC Bioinformatics 3:136), to increase statistical power of identifying relevant pathways as compared to overrepresentation analysis with gene lists. The interactive web interface enables users to visually locate their protein of interest in the curated pathway map, while the Bioconductor/R interface enables analysis to be automated for larger or more complex analyses. This workshop will include an introduction to the Reactome database and hands-on tutorials, including: 

  1. Analysis of a publicly available proteomics dataset using the interactive web interface, 

  2. Comparison of proteomics and transcriptomics data using the ReactomeGSA Bioconductor/R package, and 

  3. Analysis of a publicly available single-cell expression atlas dataset using the ReactomeGSA (Griss et al. 2020 NAR, 48(D1):D498-D503) Bioconductor/R interface.

Target Audience: 

The workshop is tailored for researchers of all levels of experience. The workshop will include step-by-step instructions on how to perform analysis on the web-based tool and also to run the R command lines on Google Colab. Some programming experiences (e.g. R in particular) is advantageous but is not essential to fully participate in this course. 

Software availability:

The online environment for the participants to run the R command lines during the hands-on part of the tutorial will be Google Colab’s R notebook (https://colab.to/r). Details will be delivered to people who have registered by email about one week prior to the workshop. 

Friday, 26th November

Clinical informatics Symposium (CAncelled)

Unfortunately, the clinical informatics symposium has been cancelled due to unforeseen circumstances. A full refund for this symposium has already been made to the credit card from which the initial payment has been made. Please contact the organisers by email conference@abacbs.org if you have any queries on the above.

Viral Metagenomics with Hecatomb

Organisers

Michael Roach (main contact) michael.roach@flinders.edu.au

Rob Edwards

Scott Handley

Sarah Giles

Workshop Time Frame

  • 10:00 - 16:00 (ACDT)

  • 10:30 - 16:30 (AEDT)

  • 07:30 - 13:30 (AWST)

Abstract
One particular virus has been at the forefront of everyone's mind recently. However, the impact from the pandemic is a drop in the ocean compared to the impact that viruses (including bacteriophages) have on our daily lives. Viruses are a core component of every microbiome and they influence every environment including human health and disease. While some are associated with disease states, most viruses are harmless or even beneficial. For instance, there is a renewed interest in the use of phages for combating the rise of antimicrobial resistance.

Viral metagenomics is fraught with challenges. Viruses are both highly diverse and poorly represented in reference databases. Viruses share large portions of sequence homology with other domains of life. Viral metagenomics studies are hence typically populated with false-positive hits while novel viruses fly under the radar. We've developed Hecatomb to address these issues and make accurate viral metagenomics accessible to anyone.

This workshop with cover an overview of the challenges associated with viral metagenomics; methods and approaches for viral enrichment and DNA extraction in the lab; a detailed overview of installing and running the Hecatomb pipeline for different platforms and usage cases; and an extensive hands-on component for visualizing and statistically interrogating your data. By the end of this workshop, you will have everything you need to perform your own viral metagenomics analysis.

What computing basics / pre-knowledge / pre-installation of software are required?

R or Rstudio with:

  • tidyr

  • dplyr

  • ggplot2

We have scheduled the hour before hand to help assist people with installing the software if they need.

What will people learn how to do?

The challenges associated with viral metagenomics; DNA extraction and viral enrichment methods; Running the Hecatomb pipeline for viral read annotation and assembly; Analysing and visualising the results in R

Running sheet (Adelaide time)

1hr 09:00 - 10:00 - OPTIONAL - Installation of required software (Michael Roach & Rob Edwards)

1hr 10:00 - 11:00 - Challenges associated with viral metagenomics (Scott Handley)

45min 11:00 - 11:45 - Viral enrichment and DNA extraction methods (Sarah Giles)

45min 11:45 - 12:30 - Running Hecatomb demonstration (Michael Roach or Rob Edwards)

1hr 12:30 - 13:30 - Lunch break

1.25hr 13:30 - 14:45 - Hands-on part 1: Loading files and filtering alignments (Michael Roach or Rob Edwards)

1.25hr 14:45 - 16:00 - Hands-on part 2: Visualisation and statistical interrogation (Michael Roach or Rob Edwards)

30min 16:00 - 16:30 - OPTIONAL - Hands-on extra help and troubleshooting (Michael Roach & Rob Edwards)