Galaxy Australia news

The October 2021 Newsletter is here.

The 2021 Galaxy Community Conference is almost upon us. GCC2021 will be held 28 June through July 10.

The June 2021 Newsletter is here. GCC2021 starts this month; James Taylor Video; plus a whole lot more.

The 2021 Galaxy Community Conference is almost upon us. GCC2021 will be held 28 June through July 10.

Several deadlines for the 2021 Galaxy Community Conference (GCC2021) have been extended.

The May 2021 Newsletter is here. Deadlines for GCC2021 and for submitted James Taylor videos have been extended, and there are updates on other upcoming events (4 in Australia), news about public Galaxy platforms, recent blog posts, training and doc updates, recent open-access Galaxy-related publications, and new releases.

The April 2021 Newsletter is out with updates on upcoming events, news about public Galaxy platforms, recent blog posts, training and doc updates, recent open-access Galaxy-related publications, and new releases.

Please join us at Galaxy's annual community gathering. It will be online, accessible, and affordable to all.

If you are a student or researcher in a developing economy, then please consider applying. Fellowships cover all conference costs. Applications are due 7 May.

If you are using, supporting, or expanding Galaxy for data-intensive science then this is an ideal way to share your work with, and gain insights from the global Galaxy Community. Abstracts are due 7 May.

We are pleased to announce the launch of the Galaxy Career Center. The Galaxy community is continually searching for new developers, bioinformaticians, system administrators, and researchers. The Career Center lists openings from around the world that use, deploy, enhance and administer Galaxy.

Galaxy is again participating in Google Summer of Code as part of the Open Genome Informatics Consortium. And we need your help, of course.

The recently completed GTN Smörgåsbord course was the largest and most global Galaxy event ever, and it was absolutely incredible. Read the report to find out how.

The Galaxy Australia support team are on leave from 5pm, Thursday, 24 December 2020 until 9am, 4 January 2021. We will respond to your request after the holiday shutdown period.

CloudBridge is a Python library that provides a consistent layer of abstraction over different Infrastructure-as-a-Service cloud providers, reducing or eliminating the need to write conditional code for each cloud.

Galaxy 20.09 has now been released!
This release includes:

Galaxy 20.05 has now been released!
This release includes:

If your use of Galaxy Australia leads to publication, please cite this paper to help promote the value of the Galaxy Australia platform to reproducible science.

JTech: Junior Training and Educational Connections Hotspot

Galaxy Australia relies on remote (to head node) deployments called Pulsar to increase the range and number of jobs that can be run on the service. The team has been allocated resources on the Nimbus cloud to deploy a dedicated COVID-19 Pulsar as part of Galaxy Australia at the Pawsey Centre that allows Galaxy users to rapidly analyse their data on published tools/workflows to further research into SARS-CoV-2.

NCI Australia and the Pawsey Supercomputing Centre are supporting the Australian and international research community undertaking COVID-19 research through provision of streamlined, prioritised and expedited access to computation and data resources.

We just lost James Taylor (1979-2020). His legacy — open, reproducible science — will continue.

Galaxy Australia has been upgraded to the latest Galaxy release. Version 20.01.
This morning after a brief planned outage, Galaxy Australia was upgraded to the latest version of Galaxy. You will notice some changes straight away - The tool menu is a bit easier to read now. Everything else is the same however!

Galaxy 20.01 has now been released!
This release includes:

A joint paper by Galaxy teams from Australia, Europe and the United States demonstrated how the COVID-19 genome data can be shared, analysed and reproduced in an efficient and transparent way. Find the paper at https://www.biocommons.org.au/galaxy-covid-19 and the workflows ready for use here in Galaxy Australia under Shared Data / Workflows.

The Genomics Virtual Lab (GVL) has had an update to version 5!

We need your input on preparing and giving Galaxy Training

Galaxy Australia has now processed over 1 million jobs! The tool run for the one millionth job was DeepTools bam coverage and completed at 8:55am on Wednesday the 29th of January 2020.

Galaxy Australia will be minimally administered during the university shutdown period from 24th December 2019 to the 2nd January 2020. During this time, only essential maintenance will be performed. No disk quota modifications, tool installations or reference data installation or upgrades will be performed.

Galaxy Australia has been upgraded to the latest Galaxy release. Version 19.09.
This morning after a brief planned outage, Galaxy Australia was upgraded to the latest version of Galaxy. You will notice some changes straight away - The tool menu is a bit easier to read now. Everything else is the same however!

Nanopore tools installed
Galaxy Australia has been updated with a new set of tools for processing Nanopore data. The tools include:

Calling all Australian life science researchers who move data!
The Australian BioCommons is a new NCRIS-funded digital capability that will enhance national bioinformatics infrastructure for environmental, agricultural and biomedical researchers. We want to know about your research data movement challenges.

Galaxy Australia moves to the new QRIS cloud stage 5 hardware
This morning after a planned outage, the Galaxy Australia main queue was moved from it's original home on QRIS cloud to their shiny new hardware! The stage 5 hardware is faster, better connected and much more flexible. This will help Galaxy Australia be more responsive to it's users as we are now able to launch bigger jobs and have them run faster.

Galaxy Australia has been upgraded to the latest Galaxy release. Version 19.05.
This morning after a brief planned outage, Galaxy Australia was upgraded to the latest version of Galaxy. You will notice some changes straight away - The colour scheme is different and the look and feel has altered. Everything else is the same however!

7 June 2019

Text processing tools have been disabled due to security concerns with one of it's dependencies. We will re-enable these tools once the security patch has been developed and applied.

Galaxy Australia has been upgraded to the latest Galaxy release. Version 19.01.
This morning after a brief planned outage, Galaxy Australia was upgraded to the latest version of Galaxy. You will notice some changes straight away - The colour scheme is different and the look and feel has altered. Everything else is the same however!

You may have noticed that Galaxy Australia was slow to respond from the 20th - 22nd of March 2019 - This has been resolved. Upon investigation the slow down was caused by a live migration of some of the backend storage to a new faster platform. The migration is mostly completed and our normal excellent level of service was resumed on the 23rd March.

Galaxy Australia has recently changed the URL for FTP uploads. If you need to upload large files to Galaxy Australia, simply log in to the FTP server at ftp://ftp.usegalaxy.org.au/ with your favourite FTP software using your Galaxy Australia credentials. For help visit the tutorial.

Galactic News March 2019

Galaxy 19.01 has now been released!
This release includes the revised UI style, addition of colorful tags, extensive workflow enhancements, and enhanced support for Singularity.

This week we have added a number of new tools to Galaxy Australia

The Galaxy Project Training Network's tutorial of the month for January/February 2019 is "Annotation of Bacterial Genomes with Prokka" chosen by our own Simon Gladman.

Galaxy Australia will be undergoing maintenance for 2 hours on the 20th February 2019 from 10:00am AEDT. It will be getting: * a new landing page * the tool panel will be updated to match usegalaxy.org and usegalaxy.eu * the backend will be upgraded to fix some job running issues

Galaxy Australia will be minimally administered during the university shutdown period from 24th December 2019 to the 2nd January 2019. During this time, only essential maintenance will be performed. No disk quota modifications, tool installations or reference data installation or upgrades will be performed.

We have added the Gemini Tools to Galaxy Australia. These tools are for doing integrative exploration of genetic variation and genome annotations. The documentation for these tools can be found here. You can find these tools under the Gemini Tools section of the Galaxy Australia tool menu.

The 2019 Galaxy Community Conference (GCC2019) will be held in be held in Freiburg, Germany, 1-6 July. The training topics that are offered are determined by the community so BY YOU!

We have started to test a few of our workflows automatically against UseGalaxy.eu. This will run all workflows monthly to ensure that the keep working and that our infrastructure works and scales well.

The Galaxy community is developing and maintaining a collection of tutorials that are designed to be interactive and are built around Galaxy: https://training.galaxyproject.org. To help highlight our tutorials and the training effort of the community, a member of the community will select every month one tutorial and explains in the Galactic Blog why they select this tutorial. This month, the Galaxy contributor of the Month!, Saskia Hilteman, selects and presents a tutorial: "Reference-based RNA-Seq data analysis", from the topic "Transcriptomics"

The good folks over at Galaxy Europe have developed a cool bit of code to help out Galaxy systems administrators. It's called gxadmin, it's available on GitHub and includes many small SQL queries that administrators run every day.

From 24th of June to 2nd of July the Galaxy Community Conference (GCC) and Bioinformatics Open Source Conference 2018 (BOSC) were meeting together in Portland, Oregon, United States. There was be two days of training, a two day meeting, and four days of intense collaboration. The meeting featured joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events. Simon and Derek were there and represented the Galaxy Australia team!

3 years ago the Galaxy community evaluated mechanism to make software installation more robust and we joined the Bioconda community, to fix the software deployment problem once and for all. Today, we are happy to annouce that the Bioconda manuscript is now published in the latest Nature Methods issue (public view). usegalaxy.org.au and many other Galaxy instance are already powered by Bioconda and you might use it daily without knowing :)