RNA-Seq Galaxy workshop at UQ

On May 1-2, 2018 we run a Galaxy workshop on RNA-Seq for QFAB. The event is fully booked. Places are still available for other Galaxy workshops.

Presentations are available for download:
Introduction to Galaxy (pptx)
Introduction to RNA-Seq (pptx)
Upload using ftp (pdf)
Galaxy workflow (pdf)

Galaxy seminar at the Ecosciences Precinct on February 6

On February 6, 2018 we run a Galaxy seminar at the Ecosciences Precinct for people from the Department of Agriculture and Fisheries. The talk provides a broad overview of Galaxy platform and Galaxy-qld server and would be of interest to people interested in analysis of high throughput sequencing data. It will follow by a Galaxy demo session focussed on data upload using ftp and genome assembly.

Slides for the seminar are available for download from Dropbox (pdf).

Introduction to Galaxy workshop at UQ

We run Introduction to Galaxy workshop at IMB, UQ on April 12, 2017, from 2 pm to 4 pm. The venue: Multimedia room 3.141 at QBP. The event is organised for IMB postgraduates and it is fully booked. The workshop is all about data in Galaxy: upload by ftp or ftp client software, move data between histories and Galaxy servers, data import from CloudStor and data libraries.

The slides from the workshop are available for download (link to pdf).

UPDATE Several Firefox Mac users have problems with right-click during the workshop. With external third party mouse put mouse cursor over Save icon; press and keep right button depressed and navigate to the appropriate line in the displayed menu, such as Save Link Location. Release of the right button puts the link into buffer. With touchpad use two fingers touch to display the menu under Save icon. Navigate to the Save Link Location link with two fingers (do not release fingers from the touchpad).

Galaxy-qld users meetup on February 1

The next meeting of Galaxy-qld users is scheduled on February 1, 2017.

Where: UQ St Lucia campus, Queensland Bioscience Precinct (QBP/IMB Building 80), Small Seminar Room 3.146 (access via ramp from Chancellor’s Place).

When: February 1, 2017, Wednesday, 10:00 AM to 11:00 AM

Topic:  de novo transcript assembly on Galaxy using Trininty.

We will cover the following:
– Overview of de novo transcript assembly workflow
– Resources available on Galaxy-qld
– QC and read trimming
– Trinity read normalization
– Assembly of transcripts using Trinity
– Counting reads

Any questions? Email Igor at i.makunin@uq.edu.au

Slides are now available for download (pdf).

Slides from Galaxy workshop at QBP


Galaxy workshop at QBP on August 17, 2016. Picture: courtesy of Nick Hamilton.

The event was fully booked, and all participants turned up for the workshop. We started with an introduction talk covering some local options available to researchers, with emphasis on Galaxy platform and Galaxy-qld server. The participants had minor problem with Galaxy-tut server at the very start of the training session, but Derek managed to fix it. The server was a bit slow in response, but the session was finished on time, with ample time left for questions.

Slides from the workshop are available as a pdf file.

Galaxy workshop at the Winter School – presentation

Galaxy workshop at the Winter School – 2016 is finished. We have 36 people registered for the event. Igor Makunin did all the talking, Derek Benson and Michal Lorenc provided help on the ground. The training was based on the GVL Basic RNA-Seq tutorial available on the GVL website, with additional introduction to Galaxy workflows. The participants have created and edited a Galaxy workflow and used it for a new analysis.

The slides from the workshop are available from the Dropbox (pdf). The personal GVL Galaxy instances used for the training will be available for the participants for one week after the workshop.

Slides from the GVL talk at IMB, UQ

On May 13, 2016 Igor gave a talk at the Institute of Molecular Bioscience about Galaxy-qld and some other resources for genomics research provided by the Research Computing Centre, UQ. The talk was followed by a short Galaxy demo session, RNA-Seq with Cufflinks package, covering a differential gene expression analysis with nextGen sequencing data. Several dozen people have attended the seminar. The slides from the talk are available from Dropbox in ppt and pdf formats.