ABACBS Education Workshops

Following on from the success of last year's Best Practices in Bioinformatics Training workshop, the ABACBS Education sub-committee will once again organise a workshop in association with the ABACBS conference, in Adelaide in November.

The  are 2 workshop Education and Training workshop on Nov 16th and 17th we have 2 topics: Using Open Science in Bioinformatics Training (1 day) and a Train-the-Trainer (1 day).

Organised by members of the ABACBS Education committee.

Using Open Science in Bioinformatics Training

Venue: SAHMRI Level 8 Boardroom, Adelaide, Australia

Date: Nov 16 2017

The Using Open Science in Bioinformatics Training day will cover aspects of open science in bioinformatics training and will consist of invited and contributed talks and panel discussions for more informal interactive sessions. What is open science?

Timetable Outline

9.00am to 10.30am:  Introduction and finding online training material (Annette McGrath)

                                Using Standards for greater reuse of material (Sonika Tyagi)

11.00am to 12.30pm:  Open access and collaboration resources for training (Paul Harrison, Adele Barugahere)

1.30pm to 3pm:         Version Control and Github (Nathan Watson-Haigh)

3.30pm to 5pm:         Licensing your material and what you need to know (Pip Griffin)

Train-the-Trainer workshop

Venue: SAHMRI Level 8 Boardroom, Adelaide, Australia

Date: Nov 17 2017

The Train-the-Trainer day will consist of a small group workshop for those who are interested in learning more about how people learn, what makes a good workshop and how to design a short course to teach to others.

Timetable Outline

9.00am to 10.30am:  Good vs bad training and trainers

11.00am to 12.30pm:  How do people learn?

1.30pm to 3pm:         How to design a good session and a good course  

3.30pm to 5pm:         Assessment and gathering feedback 

Bioconductor Masterclass

Venue: SAHMRI Level 4 Boardroom, Adelaide, Australia

Date: 16th November 2017

Overview: High-throughput sequencing technologies generate large volumes of data that present challenging bioinformatic and statistical problems. This series of hands-on tutorials introduces established and new R/Bioconductor packages and workflows for analysing high-throughput sequence data.

Course Outline

9:00-10:30am: Bioconductor Basics (Martin Morgan)

11:00am-12:30pm: RNA-seq analysis with limma, Glimma and edgeR (Charity Law)

1:30pm-2:30pm: Gene-set testing for RNA-seq data with EGSEA (Monther Alhamdoosh)

3:00pm-4:30pm: Single cell RNA-seq analysis with scPipe, scater, scran & edgeR (Shian Su)

4:30pm-5:30pm: Package Development in R/Bioconductor / Data Visualisation (Martin Morgan)

Prerequisites: The workshop assumes an intermediate level of familiarity with R, and basic understanding of biological and technological aspects of high-throughput sequence analysis. Participants should come prepared with a modern wireless-enabled laptop and web browser installed.

Intended Audience: This workshop is for bioinformaticians and computational biologists interested in using R/Bioconductor for the analysis and comprehension of high-throughput sequence data.

Third Asia-Pacific Bioconductor Meeting   

Venue: SAHMRI Level 4 Boardroom, Adelaide, Australia

Date:  17th November 2017

Overview: The Bioconductor project has undergone significant growth over the past 16 years, with over 1,300 packages for high-throughput genomic analysis included in the latest release. Many popular software tools from the project are developed by researchers from the Asia-Pacific region. To enhance collaboration and provide an avenue for networking, the Third Bioconductor Asia-Pacific meeting will be held following the ABACBS 2017 conference. This event aims to bring together researchers with an interest in the Bioconductor project to provide a forum for exchanging ideas and future plans for software development. We welcome attendance from both users and package developers (current and prospective). The meeting will consist of a number of longer talks selected from abstracts, short ‘lightning’ presentations and software demonstrations to maximize the opportunities for participants to highlight their work and share expertise.

Key dates: Email proposals for longer talks / software demos / lightning talks to (title and abstract of up to 300 words) by Friday 13th October 2017.

Travel scholarships

A number of scholarships ($500 AUD each) are available for students and Bioconductor package developers to help with the cost of travel to attend the meeting. To apply, please submit a brief statement (200 words or less) describing your interest in the meeting. If you are a package developer or maintainer please tell us the package(s) you work on. The due date for applications is Friday 13th October 2017. Please send applications to and include SCHOLARSHIP in the subject line.



Dr Matt Ritchie, Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Dr Charity Law, Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Mr Stephen Pederson, Bioinformatics Centre, The University of Adelaide, Adelaide, Australia