ABACBS-2018 Associated Symposia and Workshops

Research Computing & BioIT Meeting

Date & Time: November 26, 2-5:30

Organisers: Evan Thomas, Jason Ellul, Bernard Meade

Summary: Modern biological research institutes have personnel engaged in life science computing who are not typical researchers. We range from traditional HPC admins through dev-ops, research computing specialists, software engineers and indeed researchers advancing life science computation. Recognition of the importance of these activities is increasing however many of us working in relative isolation. In coming together at specialised meeting, we have the opportunity to meet each other, understand our common challenges and find ways to work together to meet them.

The aims of this meeting are to:

  • provide an opportunity for people to learn about research computing activities across Australia and for networks

  • articulate the challenges that we are all facing and develop ways we can work together to meet them.

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.

Workshop Program

2.00 Welcome (5 mins) – Evan Thomas

  • 2.05 Introductions (5 mins each)

    • Australian National University

    • CSIRO

    • CSL

    • Deakin University

    • Melbourne Bioinformatics

    • Melbourne Integrative Genomics

    • Melbourne University

    • Monash University

    • Pawsey Supercomputing Centre

    • Peter MacCallum Cancer Centre

    • St. Vincent's Institute of Medical Research

    • South Australian Health and Medical Research Institute

    • Walter and Eliza Hall Institute

  • 3.10 Talks (15 mins each including questions)

    • Simon Gladman – Galaxy Australia: A public bioinformatics compute resource distributed nationally

    • Brian Skjerven - Supporting Bioinformatics Workflows at Pawsey Supercomputing Centre

    • Richard Lupat - Portable Pipelines Project: Collaborative Effort to Redeploy Bioinformatics Workflows

    • Rowland Mosbergen - Alignment as a service

  • 4.10 Afternoon tea

  • 4.25 Identify breakout topics – 5 minutes

  • 4.30 Breakout session 1

  • 4.55 Breakout session 2

  • 5.20 Next steps & close

Clinical Bioinformatics Symposium

Date & Time:

November 29, 9am-12:30pm

Organisers:

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

Dr Simon Sadedin - VCGS - Melbourne, Australia

Overview

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, testing, 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 RCPA Faculty of Science .

Symposium Program

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

  • Karin Kassahn - Opportunities and challenges in clinical bioinformatics - experiences from providing a clinical genomics service            

10:00am-10:30am: Short Talks 

  • Ying Zhu - Implementation of Genomic Analysis Interface Annotation (GAIA) Platform in a diagnostic Massive Parallel Sequencing service.

  • Ken Doig - Anomaly: An extensible clinical annotation API for genomic variants.

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

11:00am-12:00pm: Short Talks 

  • Richard Lupat - Maintaining Reproducible and Robust Automated Analysis Pipelines for Clinical Cancer Sequencing

  • Satwica Yerneni - Next Generation Sequencing based Copy Number Variation (CNV) detection for Clinical Cancer diagnosis: Approach and Challenges

  • Simon Sadedin - Bioinformatics on the front line: How we deployed Ultra Rapid Genomics to enable Clinical Interventions in Real Time

  • Wishva Herath - Clinical Genomics in the cloud using Amazon Web Services (AWS)

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

  • Karin Kasshan (SA) - Head of Technology Advancement at South Australia Pathology

  • Mark Cowley (NSW) - Computational Biology Group Leader at Children's Cancer Institute

  • Natalie Thorne (VIC) - Clinical Bioinformatics and Genomics Project Manager at Melbourne Genomics Health Alliance

  • Simon Sadedin (VIC) - Head of Clinical Bioinformatics at Victorian Clinical Genetics Services

1:00-1:05 MGHA presentation

1:05-2:00 MGHA sponsored lunch

4th Bioconductor Asia Meeting and Hands-On Workshop 

Date & Time

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

Organisers

Matt Ritchie, Charity Law, Stephen Pederson

Overview

See details here.

Docker containers and Singularity images for bioinformatic pipelines

Date & Time

November 29, 9am-12:30pm

Organisers

Jan Buchmann (The University of Sydney)

Jimmy Breen (University of Adelaide)

Overview

Docker containers allow you to test and distribute simple and complex pipelines. You can write pipelines with different dependencies without the need to install them on your machine. Users can then pull your pipelines or tools and start using them without having to worry about dependencies or adventurous installation instructions. If your tool or pipeline can run on a HPC cluster, you can also deploy them as Singularity images, a more secure variant of docker containers. The workshop will introduce you to Docker Containers and Singularity Images. You will learn how to create, run, and distribute them using typical biological tasks as examples. Participants are invited to bring their own pipelines they wish to "Dockerize" in the last part of the workshop.

Target Audience

You have written an amazing analysis pipeline which depends on your own and external libraries. You incorporated external software for specific steps and the  pipeline requires the newest version of your favorite programming language due to THIS feature. You spent a day to write and test the installation instructions on your own machine. A few days later, you discover that only few users read the README, several complain about weird dependencies, others cannot install dependencies due to different reasons. You consider to skip the Reviewer comments and discover that your cluster got updated and you have to fix all dependencies for your own pipelines as well as for external software. If any of these scenarios sounds familiar to you, this could be your workshop.

What to bring

Laptop with administrative privileges. Installed Docker [0] and Singularity [1] for your OS. Assuming: experience with the command-line of your OS (the workshop will use examples using the Unix command-line), familiarity with git and ssh.

References

[0]: https://store.docker.com/search?type=edition&offering=community

[1]: https://singularity.lbl.gov/all-release

Machine learning to deep learning and beyond: A Practical Introduction to Machine and Deep Learning Techniques and their uses in Healthcare

Date

November 29, 2pm-5:30pm

Organisers

Tansel Ersavas, Garvan Institute of Medical Research

Angela Yin, Garvan Institute of Medical Research

Overview

Recently, Machine learning and Artificial Intelligence (AI), and especially one area of "machine learning" called "deep learning", gained prominence after being successfully applied to many different fields, and proved to be on par or in some cases better than humans in a wide variety of areas from game playing to medical diagnosis.

In this workshop, we'll introduce basic concepts of machine learning and deep learning techniques.

Machine learning is a branch of Artificial Intelligence that lets machines "learn" from data rather than being programmed by programmers to analyse the data. Deep learning is a branch of machine learning that is inspired by how brains work.

After a quick recap of the history, we will go through some machine learning and deep learning techniques and how they are currently being used for a wide variety of problems from genome analysis, medical and microscopic image diagnosis, and natural language processing to real-time monitoring of patients' vitals. We'll conclude the workshop with a brief look at the near future and opportunities for medical researchers to benefit from these developments and how they can be involved in this revolution.

Best Practices in Bioinformatics Software Development

Date:

November 30, 9am-5:30pm

OrganiserS

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

Overview

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).