Workshops

The 2019 ABACBS/GIW conference will be held in Sydney from 9-11th December. The COMBINE/AYRCOB Student Symposium will be on the 9th December. It will be preceded by the AMSI BioInfoSummer meeting from 2-7th December, making for an exciting concentration of bioinformatics and computational biology in Sydney at the end of the year.

As in previous years, the one day following the main conference (12th December) 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.

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 the workshop(s) without registering for the conference.

Questions on the workshops should be emailed to natalie.twine@csiro.au and kitty.lo@sydney.edu.au

NEWS

The Machine Learning Applications Using Amazon Cloud Workshop has been cancelled and is now replaced by the Single Cell Rna-Seq Data Analysis On The Cloud Workshop outlined below. This workshop will primarily use the Amazon Cloud for single cell data analysis. Participants who had previously registered for the Machine Learning workshop has their registrations transferred to the Single Cell RNA-Seq Data Analysis On The Cloud Workshop automatically without any changes to your current registration. Current registrants also have the option to request a cancellation and refund without tickets to attend the replacement workshop. For refunds please contact the current ABACBS Secretary Sebastian Kurscheid (Sebastian.Kurscheid@anu.edu.au).

Costs: Per Half Day Workshop: $40 (member), $50 (non-member)

REGISTRATION FOR WORKSHOPS IS NOW CLOSED.

Catering: Only morning and afternoon teas will be included as part of the workshop. Participants are encourage to purchase their own lunch at a variety of restaurants nearby the UTS precinct.

Location

University of Technology Sydney (UTS), Building 10 (CB10)

The UTS building 10 is within walking distance from the Central Train station and nearby bus stops.

Google Map: https://goo.gl/maps/X35VNihT4fMnnb917

Classrooms: CB10.03.480, CB10.03.470, CB10.03.450

Morning 9 am -12 noon (except Clinical Bioinformatics Symposium 9 am - 1 pm)

Single Cell RNA-Seq Data Analysis On The Cloud (Morning, Half Day)*

ROOM: CB10.03.450

Computational processing of large single cell RNA-seq (scRNA-seq) data poses many challenges, including storing, processing, and analysing potentially hundreds of gigabytes of data using programs that require high CPU and memory demand. This can be especially challenging if local computational resources are limited. In this workshop, we will explore how to use commercial cloud computing resources to construct scalable computational processing pipelines for scRNA-seq data analysis, ranging from sequence read alignment, feature quantification, transcript assembly, and downstream analyses such as dimensionality reduction, clustering, and visualisation. In this hands-on session, attendees will gain practical experience in setting up utilising cloud computing resources to process data generated by full-length scRNA-seq (e.g., Smart-seq) and 3’-end enriched (e.g., 10X Genomics) scRNA-seq data.

REQUIREMENT: Attendees need to bring their own computer, and is comfortable to work in a command-line environment. Experience in using Amazon Web Services is helpful.

INSTRUCTORS: Mr Gordon Qian and Ms Xiunan Fang, University of Hong Kong

Snakemake Workshop (Morning, Half Day)*

ROOM: CB10.03.480

CONVENER: Dr. Nathan Watson-Haigh

OVERVIEW

Recent years have seen a groundswell of support in the bioscience community for improved reproducibility of data analyses. Large analysis workflows are fragile ecosystems of software tools, scripts and dependencies. One solution to these issues is the use of a workflow management system such as Snakemake, capable of being executed across different computing environments (laptop/desktop to High Performance Computing).

Nathan will cover the core concepts of Snakemake with a focus on reimplementing a bash script for performing quality control, trimming and alignment of Illumina data against a reference sequence. In doing so, workshop attendees will be capable of starting to implement their own workflows following the workshop.

PREREQUISITES

• Experience with at least 1 scripting language

• Experience with the Linux command line

• Internet enabled laptop with an SSH client installed

Clinical Bioinformatics Symposium (Morning, Half Day)*

Click Here to Download the Program

ROOM: CB10.03.470

ORGANISERS

• A/Prof Mark Cowley - Children’s Cancer Institute, Sydney, Australia

• Dr Mark Pinese - Children’s Cancer Institute, Sydney, Australia

OVERVIEW
Clinical bioinformatics is an emerging area of patient-focused science, with a focus on the development of methods for acquiring, storing, organising and analysing biological data that supports the delivery of patient care. This is a rapidly evolving and growing field in Australia, and yet the various skills and challenges associated with it are often unknown / unappreciated.
Building on last-year’s successful event held in Melbourne, this mini-symposium will showcase the profession from the perspective of clinical bioinformaticians, many of whom are now working outside of traditional academia. Topics including clinical-grade methods development, accreditation, validation, testing, robustness and quality control for clinical applications will be discussed.

A discussion panel with experienced clinical bioinformaticians will also raise awareness about the myriad career opportunities and their corresponding paths.

We encourage you to select the ‘clinical bioinformatics’ option when you submit your abstract to GIW/ABACBS for consideration to present your work at this year’s symposium.

Afternoon 2 - 5 pm

GWAS, Machine Learning and the Cloud (Afternoon, Half Day)*

ROOM: CB10.03.470

CONVENERS: Dr. Natalie Twine, Dr. Arash Bayat

OVERVIEW

In this workshop, you will learn how to setup a Jupyter notebook on AWS cloud with VariantSpark and Hail installed. You will learn to develop a GWAS analysis pipeline including quality-control, GWAS and post GWAS analysis.

Please bring your own laptop for the hands-on components of this workshop.

Proteomics Data Analysis Workshop (Afternoon, Half Day)*

ROOM: CB10.03.480

CONVENER: Prof. Jürgen Cox

OVERVIEW

This workshop provides an introduction to the computational proteomics platform MaxQuant and the downstream bioinformatics platform Perseus. The first part provides theory and background information to the workflows and algorithms while the second part is hands-on and participants will be able to apply the tools to some real-world examples. Participants should bring Windows laptop computers to participate in the practical parts.

Please bring your own laptop for the hands-on components of this workshop.

REGISTRATION FOR WORKSHOPS IS NOW CLOSED.

* The workshop will only run if more than 10 people registered. Full refund will be provided to all registrants if the workshop is cancelled due to low number of participants.