ABACBS-2018 Associated Symposia and Workshops

Research Computing & BioIT Meeting

Date: November 26, 2-5:30

Organisers: Evan Thomas, Jason Ellul, Bernard Meade

Summary: This meeting is for research computing professionals, HPC sys-ads or dev-ops working in BioIT or other interested people to interact and discuss issues and solutions in life science computing. Catering has been generously provided by the Walter and Eliza Hall Institute Research Computing Centre and Information Technology Service, so this event is free. Please contact Tony Papenfuss for the coupon and use this to register.

Clinical Bioinformatics Symposium


November 29, 9am-12:30pm


Ms Roxane Legaie - Pathology Department, Peter MacCallum Cancer Centre - Melbourne, Australia

Dr Simon Sadedin - VCGS - Melbourne, Australia

Ms Mhairi Clout - Australian Translational Genomics Centre, QUT - Brisbane, Australia


Clinical Bioinformatics is a new and fast growing field in Australia, and yet the various skills and challenges associated with it are often unknown / unappreciated.

This mini-symposium will showcase the profession outside the academic world with a number of talks from clinical bioinformaticians around topics such as accreditation, validation, tetsing, quality control and novel approaches for clinical applications.

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

Invited Speaker

We are pleased to announce that Dr Karin Kassahn from SA Pathology will be our keynote speaker to launch the event.

Karin is passionate about innovative diagnostics and translational research. She obtained her PhD in marine genomics from James Cook University in 2007 and pursued post-doctoral positions at the Institute for Molecular Bioscience, UQ, in comparative genomics, bioinformatics and medical genomics. She was an active member of the International Cancer Genome Consortium where her research focused on somatic mutation detection from next-generation sequencing. In 2013 she took up the position of Head of Technology Advancement at SA Pathology to implement NGS in clinical diagnostics. In her current role, Karin is overseeing the development and validation of pipelines for diagnostic use and standardisation of analysis approaches. She is performing research into the molecular genetics of childhood disorders and tumour profiling for identification of targeted therapy. Karin assists in the development of standards of practice in the field of medical genomics and is a Fellow of the Faculty of Science (RCPA).

Opportunities to present your work

A number of slots for short talks (15-30 minutes) are available. If you would like to present your work, please select the relevant option in the online submission system. Email your presentation title and an abstract of up to 300 words to roxane.legaie@petermac.org by Friday 28th September 2018 to be considered.

Tentative schedule

9:00am-10:00am: Introduction & Keynote Presentation                     

10:00am-10:30am: Short Talks

10:30am-11:00am: Morning Tea (provided)

11:00am-12:30pm: Short Talks

12:30pm-1:00pm: Discussion panel        


4th Bioconductor Asia Meeting and Hands-On Workshop 

Date: November 29-30, 9am-5:30pm

Organisers: Matt Ritchie, Charity Law, Stephen Pederson

Summary: See details here.

Docker Containers and Singularity Images for Bioinformatic Pipelines Workshop

Date: November 29, 9am-12:30pm

Organisers: Jan Buchmann, Jimmy Breen

Summary: TBA

Machine Learning for Healthcare Workshop

Date: November 29, 2pm-5:30pm

Organisers: Tansel Ersavas, James Ferguson, Angela Yin

Summary: TBA

Best Practices in Bioinformatics Software Development


November 30, 9am-5:30pm


Bernie Pope, bjpope@unimelb.edu.au, University of Melbourne

Daniel Cameron, cameron.d@wehi.edu.au, WEHI

Anna Syme, anna.syme@unimelb.edu.au, University of Melbourne


Software development is a central part of bioinformatics, but for many reasons software quality is not always prioritised, leading to problems in maintenance, usability and reproducibility. Adopting software engineering best practices at the beginning of a project can address these problems, but this is often not done due to lack of time and/or experience. This workshop covers the essentials of good programming practices and provides you with tools and knowledge to build high quality bioinformatics software from the outset. In the first half of the workshop we will introduce a tool for quickly creating new software projects with important features and infrastructure already included. You will use this tool to initialise a new project including a fresh repository on GitHub. In the second half of the workshop we will introduce a set of software engineering practices designed for large-scale software systems that are suitable for bioinformatics programs written by a single author. We will apply these techniques to add new features to the software project created in the first half of the workshop. By the end of the day you will have built a robust bioinformatics project that can be extended with your own functions or re-implemented in other languages.

Target audience

Bioinformaticians with beginner to intermediate level of programming experience who want to apply good software engineering practices in their daily work. Experience with the Unix command-line is assumed.  Basic familiarity with Python (or similar languages) is an advantage. What to bring: Laptop with Unix (e.g. an Apple Mac or Linux). Windows users: please install Putty. Please set up a GitHub account (free, https://github.com/join).