December 2019 Galactic News
Events, Pubs, Blogs, Platforms, Tutorials, Doc, Jobs, Releases, and Platypi too.
December 9th 2019
The December 2019 Galactic News is out:
- 12 Upcoming Events
- India, PAG, HTS, single cell/microbiome, Barcelona, and more
- 191 new publications
- Two new blog posts
- g:Profiler, GalaxyP
- Galaxy Platform News
- Systems biology, Laniakea, OpenRefine, ...
- Training material and doc updates
- defining data types, citing GTN, Windows, account help, metatranscriptomics, Galaxy for everyone
- with 5 organizations in Denmark, France, US, US, Germany
- Galaxy 19.09 is out
- And other news too
If you have anything to include to next month's newsletter, then please send it to firstname.lastname@example.org.
Galaxy (especially Galaxy Australia will be featured in a workshop and a plenary talk at the International Symposium on Bioinformatics 2019 (InSyB2019) being held December 21-22, 2019 at Hans Raj Mahila Maha Vidyalaya, Jalandhar, Punjab, India. Registration and abstract submission are still open.
Galaxy will be at Plant and Animal Genome XXVII (PAG 2020), in San Diego, California, United States, January 11-15. This includes a hands-on Galaxy Workshop (highlighting the new Excellence in Breeding platform) and many talks and posters featuring Galaxy.
This week-long Galaxy workshop in Freiburg will introduce participants to high-throughput data analysis with Galaxy. Space is limit, and applications are competitive. Apply by 19 December.
Galaxy will be at 2020 ABRF meeting, in Palm Springs, California, United States, February 29 through March 3. This includes a full day hands-on Galaxy Workshop about using Galaxy with your single cell and microbiome data. ABRF is the annual conference for technology-enabled multidisciplinary research.
Registration is now open, but space is limited.
This week-long hands-on training will feature what you need to know to set up your own production quality Galaxy server. Registration will open later this month.
- 12 upcoming events
- on 3 continents, plus online
- in India, US, Belgium, Germany, France, Spain, and the UK.
191 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in the last month. There were seven Galactic and Stellar publications added, and all seven of them are open access:
Kumar, A., Grüning, B., & Backofen, R. (2019). BioRxiv, 838599. doi: 10.1101/838599
Wibberg, D., Batut, B., Belmann, P., Blom, J., Glöckner, F. O., Grüning, B., … Kohlbacher, O. (2019). F1000Research, 8, 1877. doi: 10.12688/f1000research.20244.1
Perez‐Riverol, Y., & Moreno, P. (2019). PROTEOMICS, 1900147. doi: 10.1002/pmic.201900147
Demko, M., Chrást, L., Dvořák, P., Damborský, J., & Šafránek, D. (2019). Microorganisms, 7(11), 553. doi:10.3390/microorganisms7110553
McGowan, T., Johnson, J. E., Kumar, P., Sajulga, R., Mehta, S., Jagtap, P. D., & Griffin, T. J. (2019). BioRxiv, 842856. doi: 10.1101/842856
Kumar, P., Johnson, J. E., Easterly, C., Mehta, S., Sajulga, R., Nunn, B., … Griffin, T. J. (2019). BioRxiv, 843078. doi: 10.1101/843078
Monnerie, S., Petera, M., Lyan, B., Gaudreau, P., Comte, B., & Pujos-Guillot, E. (2019). Metabolites, 9(11), 250. doi: 10.3390/metabo9110250
Publications are tagged with how they use, extend or reference Galaxy. The past month's pubs were tagged as:
Two new entries in the past month, both related to UseGalaxy.eu..
By Ivan Kuzmin. gProfiler is a toolset for functional enrichment analysis and conversions of gene lists.
By Ben Orsburn. The arguments are building up for why you need this.
The Galaxy Platform Directory lists resources for easily running your analysis on Galaxy, including publicly available servers, cloud services, and containers and VMs that run Galaxy. There are many new platforms this month:
And the ProteoRE group is hiring too. See below.
The account creation documentation was expanded by Jennifer Hillman-Jackson to cover additional situations and help resources.
Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the functional analysis of genes expressed by the microbiome. This tutorial uses the ASaiM workflow (Batut et al. 2018) to study a time-series analysis of a microbial community from (Kunath et al. 2018).
Hey Good People! It's hard to find good people, such as yourself, but surely you know good people who could help the good people below fill their open positions. (And if you have a Galaxy-related opening then please send it to outreach @ galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.)
Biotech Research & Innovation Centre (BRIC) Bioinformatics Core Facility, University of Copenhagen.
Maintain, update, upgrade and provide user support for a local version of a Galaxy server. (And other stuff too.) Applications close 15 December.
CEA/INSERM/UGA, Grenoble, France. Conception d’un workflow protéogénomiques: identifiez, optimisez, et le cas échéant, développez les outils necessaires dans Galaxy; ils seront déployés sur le serveur ProteoRE. Idéalement, le workflow sera documenté sous la forme de leçons intégrées dans le "Galaxy Training Network".
The Plant Computational Genomics lab in the Department of Ecology and Evolutionary Biology at the University of Connecticut seeks motivated MS and PhD students to join the lab in the Summer/Fall 2020.
The 19.09 release of Galaxy is out and full of new features:
- Embedded reports in workflows
- New visualizations
- Lots of new datatypes.
- A new type of interactive Galaxy tool has been implemented
- A New Toolshed Client Interface
A US$3.5M NSF grant has been awarded to Penn State researchers to enable Galaxy-based tools to use GPUs. Speeding up science, by 10-100x.
And that is quite possibly the coolest end of year news item we have ever had.
Thanks for an excellent year, and looking forward to 2020.