Galaxy Australasia Workshop 2014 (GAW 2014)


    The 1st Galaxy Australasia Workshop 2014 (GAW 2014) was held in Melbourne, Australia on 24 and 25th March 2014. The Galaxy Australasia Workshop was a great opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 ran 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne. GAW 2014 also included poster session and keynote speakers. You should attend to: Present your work! Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets. Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them. Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction. Learn how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics) how to share, publish, and reuse your analyses with Galaxy how to perform and enable your users to perform common, yet complex, analyses using Galaxy * when and how to use Galaxy on the Cloud # Program ## Day 1, 24th March 2014
    Time Title
    10:00-10:10 Welcome. Logistics, etc.
    Organising Committee
    10:10-10:35 Keynote: Reproducible complex analyses as a scientific commodity: Why Galaxy matters
    Ross Lazarus (download pdf slides)
    10:35-11:00 Morning Tea
    11:00-11:30 Launching your (small) Galaxy instance on the Research Cloud
    Andrew Lonie Live Demo - no slides. Follow the Launch GVL Basic Guide
    11:30-13:00 Galaxy 101 - a tutorial
    Mark Crowe (download pdf slides)
    13:00-13:50 Lunch Break
    During lunch, assistance will be available to help attendees set up a Galaxy on GVL
    13:50-14:05 Tips and tricks open mic
    Chair: Ira Cooke
    14:05-14:40 Galaxy in the wild: Galaxy Architecture and Supporting Production Level Genomics
    Nate Coraor (download PDF slides)
    14:40-15:20 Introduction to the Tool Shed: Tight dependency control for reproducible analysis
    Ross Lazarus (download pdf slides)
    15:20-15:50 Afternoon Tea
    15:50-16:20 CloudMan Project
    Enis Afgan (download pdf slides)
    16:20-17:00 Setting up and administering Galaxy - panel discussion
    Stephen McMahon, Nate Coraor, Enis Afgan
    ### Posters Posters to be displayed throughout the day:
    Poster
    Microbial Community Analysis of Indonesia Tempeh Employing Metagenome Galaxy
    Adi Yulandi, Faculty of Biotechnology Atma Jaya Catholic University of Indonesia (download pdf poster)
    Training with the GVL
    Simon Gladman, VLSCI - LSCC (download pdf poster)
    Cloud-based Image Analysis and Processing Toolbox
    Tomasz Bednarz, CSIRO (download pdf poster)
    ## Day 2, 25th March 2014
    Time Title
    09:00-09:10 Welcome. Logistics, etc.
    Organising Committee
    09:10-09:50 Keynote: Galaxy - past, present and future
    Nate Coraor (download PDF slides)
    9:50-10:30 Bioinformatics Stream
    9:50 Using Galaxy for Proteogenomics
    Ira Cooke (download PDF slides)
    10:10 shRNA-seq analysis in Galaxy
    Matthew Ritchie (download PDF slides)
    10:30-11:00 Morning Tea
    11:00-12:30 General Stream
    11:00 The Australian Genomics Virtual Lab
    Andrew Lonie (download pdf slides)
    11:30 Building a Galaxy user community for a fully supported Galaxy service
    Annette McGrath (download PDF slides)
    11:50 Galaxy with GenomeSpace
    Yousef Kowsar
    12:10 Using Galaxy cloud servers for command-line analyses
    Clare Sloggett (download PDF slides)
    12:30-13:30 Lunch Break
    13:30-14:50 Application Stream
    13:30 Cellular Imaging tools on NeCTAR cloud
    Yulia Arzhaeva (download pdf slides)
    13:50 Secure Cloud Data Storage for Galaxy Workflows
    Carsten Friedrich (download pdf slides)
    14:10 CSIRO in house tools and dealing with Big data
    Philippe Moncuquet (download pdf slides)
    14:30 Galaxy service at CSIRO
    Stephen McMahon (download pdf slides)
    14:50-15:30 Afternoon Tea
    15:30-16:10 Genomics VL Stream
    15:30 Building, Launching and Maintaining Galaxy on the Australian Research Cloud
    Ron Horst (download pdf slides)
    15:50 Scaling the GVL: Empirical Evaluation of Galaxy Scalability Characteristics
    Nuwan Goonasekera (download pdf slides)
    16:10-17:00 Panel
    # Venue(s)
    Melbourne Convention Centre

    GAW 2014 was held in Melbourne, Australia on 24 and 25th March 2014. The first day (Monday) was at Monash University, MBI Auditorium (Building 220), 770 Blackburn Rd, Clayton (map); next to the Australian Synchrotron.
    For the 2nd day (Tuesday) we moved downtown to the Melbourne Convention Centre, the venue for the Computational and Simulation Sciences and eResearch.

    Travel Info

    Airport to/from City

    Taxi / Bus / Skybus

    myki public transport

    It may be worth buying a myki card; then you will have no issues using train/bus to Clayton and trams around the city. $6 for the card, plus $12.12 bus/train return to Clayton campus, plus trams around the city.

    Monday: Clayton MBI Auditorium, 770 Blackburn Rd

    The Australian Synchrotron is about 15 minutes walk from the Monash University Clayton Campus Bus Loop. Travelling to Clayton Campus and Public Transport to Clayton Campus - Detail

    Tuesday: Melbourne Convention Centre

    Directions

    Consider Melbourne City Bikes, though the closest Bike Share Station is across the river.

    Promotion

    Help get the word out about GAW 2014.

    Please print, post and distribute the conference flier
    at your organization, and or events.

    The conference logo is available in 200 pixel, 400 pixel, and 600 pixel resolutions for inclusion on web sites, presentations, and posters.

    Twitter Hashtag

    Please use #gaw2014 as the Twitter hashtag for the meeting.

    Conference Report

    CSIRO

    The first Galaxy Australasia Workshop was held on Monday 24th and Tuesday 25th March. Conference venues and catering were provided by CSIRO (Australia's national science agency) so attendance was free.

    Day 1 was held at the Monash Biomedical Imaging Auditorium at Monash University. The large auditorium did make the audience seem small, and perhaps the distance of the venue from the Melbourne CBD discouraged those few who had registered but did not attend.

    Ross Lazarus (Baker IDI/Galaxy) opened in his usual entertaining manner and told us Why Galaxy matters: Reproducible complex analyses as a scientific commodity.

    GVL

    Andrew Lonie (VLSCI/GVL), despite the usual risks of doing anything live, successfully demonstrated how to Launch a bioinformatics analysis server installed with Galaxy on the Australian Research Cloud and a handful of attendees followed along and launched their own GVL Galaxy server.

    QFAB

    Mark Crowe (QFAB/GVL) presented a tutorial on using Galaxy, aimed at the members of the audience new to Galaxy.

    The tips and tricks open mic session went well, with even some experienced Galaxy users learning a few things they hadn’t known.

    The rest of the afternoon consisted of some more presentations and then a panel discussion about Setting up and Administering Galaxy, which again worked quite well given our small audience size. This reflects on the level of engagement of all those present.

    The day closed amidst the usual scrum of organising taxis and public transport to return to accommodation and the evening’s ad hoc social events.

    Atma Jaya Catholic University of Indonesia

    Three posters were displayed, including "Microbial Community Analysis of Indonesia Tempeh Employing Metagenome Galaxy" which was brought to us by some enthusiasts all the way from Indonesia.

    Day 2 was held in the Melbourne Convention Centre, alongside CSIRO’s Computational and Simulation Sciences and eResearch conference.

    Nate Coraor, our special guest from the Galaxy Project, entertained us with a look at working versions of Galaxy from the past, and updated us on Galaxy in the present and coming in the future.

    Latrobe University WEHI

    Then two presentations about using Galaxy for Bioinformatics Analysis: Using Galaxy for Proteogenomics from Ira Cooke (Latrobe) and shRNA-seq analysis in Galaxy from Matthew Ritchie (WEHI).

    The GVL Project and CSIRO each gave us a few presentations about their progress with Galaxy, including CSIRO’s Philippe Moncuquet explaining how CSIRO is managing the large volumes of data.

    Nectar

    Further interesting talks included Yousef Kowsar (VLSCI/GVL) showing us progress with an Australian Research Cloud version of GenomeSpace integration with Galaxy, Clare Sloggett (VLSCI/GVL) demonstrating some utilities that enhance the GVL command line servers, Yulia Arzhaeva (CSIRO) showing a Galaxy implementation of Cellular Imaging tools rather than Bioinformatics Tools and Carsten Friedrich (CSIRO) showing a Galaxy Tool interface to Secure Cloud Data Storage.

    Australian Bioinformatics Network

    David Lovell (CSIRO), as representative of the Australian Bioinformatics Network, closed the conference by working with us to develop a worthwhile mind map (pdf) of actions we would take as a result of attending the Conference.

    Slide presentations appear on the GAW2014 conference programme.