The South African National Bioinformatics Institute’s Peter van Heusden served as the Scientific Programme Chair for the 2021 Galaxy Community Conference (GCC2021).
Galaxy is “open, web-based platform for accessible, reproducible, and transparent computational research” that researchers & software engineers at the Institute have been contributing to since 2010.
The Galaxy Community Conference is an annual meeting of developers, trainers and users of the Galaxy platform and like so many events, this year’s meeting was held online rather than, as originally planned, in Belgium. Traditionally the Galaxy conferences have rotated between venues in Europe and North America with the COVID-19 pandemic largely shutting down international travel, the 2020 meeting (held together with the Bioinformatics Open Source Conference as BCC2020) and the more 2021 conference both were held on the Internet using the Remo social platform. Since the videos were prerecorded, they are all online. Those who want to watch them should browse the conference programme. Unfortunately the virtual poster presentations could not be automatically exported from Remo, so while some presenters linked to copies of their posters (on e.g. F1000 Research), some of the other posters were lost.
Highlights of GCC2021 included talks on Galaxy tools for analysing SARS-CoV-2, the virus that causes COVID-19 and a number of talks on the use of Galaxy in a pathogen genomics and public health context. There is now a nascent Galaxy Public Health community (see links below) and the previous Galaxy Microbiome community has re-focused to be Galaxy Micro, and focus on microbial bioinformatics using Galaxy. A summary of some interesting talks at GCC2021 is in the table below.
The GCC2021 conference was preceded by a week of training activities that, once again, featured the tutorial on M. tuberculosis variant analysis using Galaxy. This tutorial, with an accompanying video on genomic variant discovery in M. tuberculosis was also featured in the Galaxy Smörgåsbord global training course (held in February 2021). By making openly accessible tutorials and training materials like this, SANBI is promoting its work on tools for M. tuberculosis bioinformatics, originally sponsored by the MRC funded COMBAT TB project.
Highlights of the Galaxy Community Conference (according to Peter van Heusden)
| Topic | Link | Code, Comments, Etc |
| Supporting the COVID 19 Data portal viral data cleaning from human reads and submission to ENA | https://gcc2021.sched.com/event/jm5V/supporting-the-covid-19-data-portal-viral-data-cleaning-from-human-reads-and-submission-to-ena | ENA Upload tool: https://github.com/usegalaxy-eu/ena-upload-cli Metadata added via spreadsheet, genomic data as Galaxy datasetsHuman reads removed using https://github.com/Finn-Lab/Metagen-FastQC |
| Galaxy as a global platform for the analysis of SARS-CoV-2 sequence variants | https://gcc2021.sched.com/event/jm5Y/galaxy-as-a-global-platform-for-the-analysis-of-sars-cov-2-sequence-variants | Use usegalaxy.* resources to analyse sequences specified by URL, getting the full power of the Galaxy public servers to analyse your SARS-CoV-2 data. |
| Using Galaxy File Source Plugins to Work with Remote Data including Applications | https://gcc2021.sched.com/event/ih0X/using-galaxy-file-source-plugins-to-work-with-remote-data-including-applications | Better integration between Galaxy and Cloud-hosted data. Still involves “copy into Galaxy” step but this is important progress in making Galaxy more “cloud-native” |
| Enhancing the Whole Workflow Experience from Development through Publication and to Execution | https://gcc2021.sched.com/event/jm5z/enhancing-the-whole-workflow-experience-from-development-through-publication-and-to-execution | Lots of comments on behind-the-scenes enhancement on Galaxy workflows including scalability, the “workflow report” etc. |
| Introducing the Intergalactic Workflow Commission | https://gcc2021.sched.com/event/jm62/introducing-the-intergalactic-workflow-commission | A workflow-focused collaboration – https://github.com/galaxyproject/iwc – like IUC but for workflows. Still in process of building tooling, best practices, etc. Relates to WorkflowHub.EU and Dockstore, better tooling for these coming to Galaxy. |
| Publication of BioCompute Objects (IEEE-2791-2020) created from Galaxy workflow invocations | https://gcc2021.sched.com/event/jm65/publication-of-biocompute-objects-ieee-2791-2020-created-from-galaxy-workflow-invocations | FDA-originated project to enhance evidence from computational methods |
| The WorkflowHub – a registry for workflows | https://gcc2021.sched.com/event/jm6B/the-workflowhub-a-registry-for-workflows | About WorkflowHub.EU |
| The “ARIES Genomics” Italian public health surveillance system | https://gcc2021.sched.com/event/jm7e/the-aries-genomics-italian-public-health-surveillance-system | ARIES Galaxy and IRIDA from the Istituto Superiero di Sanità, focused on “surveillance of infectious epidemics, foodborne outbreaks and diseases at the animal-human interface” |
| Fostering Public Health Bioinformatics and Collaboration with GalaxyTrakr | https://gcc2021.sched.com/event/jm7h/fostering-public-health-bioinformatics-and-collaboration-with-galaxytrakr | The FDA’s GalaxyTrakr system. Also see: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07405-8 |
| W-3.7: A flexible Galaxy-based platform for the analysis of microbial WGS data in public health | https://gcc2021.sched.com/event/k5MH/w-37-a-flexible-galaxy-based-platform-for-the-analysis-of-microbial-wgs-data-in-public-health | Poster on the Sciencesano Galaxy. Unfortunately code is not open source. See also https://pubmed.ncbi.nlm.nih.gov/33789960/ |
| Tu-3.3: Practical aspects of implementing the IRIDA system as a solution for One Health bioinformatics analyses | https://gcc2021.sched.com/event/k5Lt/tu-33-practical-aspects-of-implementing-the-irida-system-as-a-solution-for-one-health-bioinformatics-analyses | Poster on how IRIDA has been implemented from Dr Karin Lageson’s lab at the Norwegian Veterinary Institute |
| W-4.2: Driving workforce transition in Australian life science research | https://gcc2021.sched.com/event/kGcz/w-42-driving-workforce-transition-in-australian-life-science-research | Interesting poster on how Galaxy has been part of enabling the transition of Australian life science researchers to computational methods. Poster is here on F1000 Research |
| Galaxy Training Network (GTN) Community Update | https://gcc2021.sched.com/event/ihqA/galaxy-training-network-gtn-community-update | The Galaxy Training Network has really grown in recent years. The GTN can be found at https://gitter.im/Galaxy-Training-Network/Lobby, https://training.galaxyproject.org/ and https://github.com/galaxyproject/training-material. Material from the early-2021 Galaxy Smörgåsbord can be found here: https://shiltemann.github.io/global-galaxy-course/workshop. And GTN now hosts its first tutorial in Spanish. |
| The Galaxy Public Health Community | https://gcc2021.sched.com/event/jm7Y/the-galaxy-public-health-community | The community now has a chat channel: https://gitter.im/galaxyproject/Public-Health and mailing list |