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December 2019 Galactic News

Events, Pubs, Blogs, Platforms, Tutorials, Doc, Jobs, Releases, and Platypi too.

Galaxy News

The December 2019 Galactic News is out:

If you have anything to include to next month's newsletter, then please send it to outreach@galaxyproject.org.

Events

Galaxy @ InSyB 2019
Galaxy @ InSyB 2019

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 @ PAG 2020
Galaxy @ PAG 2020

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.

And there will be a GMOD Codefest before PAG and an NCBI Codeathon after PAG.

9th Galaxy workshop on HTS data analysis
9th Galaxy workshop on HTS data analysis

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 @ ABRF 2020
Galaxy @ ABRF 2020

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.

Galaxy Admin Training 2020
2-6 March: Galaxy Admin Training 2020

Save these dates! The next Galaxy Admin Training will be offered 2-6 March at the Barcelona Supercomputing Center.

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.

Upcoming Events
Upcoming Events

There are

  • 12 upcoming events
  • on 3 continents, plus online
  • in India, US, Belgium, Germany, France, Spain, and the UK.

Publications

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:

[Tool recommender system in Galaxy using deep learning](https://doi.org/10.1101/838599)

Kumar, A., Grüning, B., & Backofen, R. (2019). BioRxiv, 838599. doi: 10.1101/838599

[The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR](https://doi.org/10.12688/f1000research.20244.1)

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

[Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines](https://doi.org/10.1002/pmic.201900147)

Perez‐Riverol, Y., & Moreno, P. (2019). PROTEOMICS, 1900147. doi: 10.1002/pmic.201900147

[Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway](https://doi.org/10.3390/microorganisms7110553)

Demko, M., Chrást, L., Dvořák, P., Damborský, J., & Šafránek, D. (2019). Microorganisms, 7(11), 553. doi:10.3390/microorganisms7110553

[Multi-omics Visualization Platform: An extensible Galaxy plug-In for multi-omics data visualization and exploration]( https://doi.org/10.1101/842856)

McGowan, T., Johnson, J. E., Kumar, P., Sajulga, R., Mehta, S., Jagtap, P. D., & Griffin, T. J. (2019). BioRxiv, 842856. doi: 10.1101/842856

[A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases](https://doi.org/10.1101/843078)

Kumar, P., Johnson, J. E., Easterly, C., Mehta, S., Sajulga, R., Nunn, B., … Griffin, T. J. (2019). BioRxiv, 843078. doi: 10.1101/843078

[Analytic Correlation Filtration: A New Tool to Reduce Analytical Complexity of Metabolomic Datasets](https://doi.org/10.3390/metabo9110250)

Monnerie, S., Petera, M., Lyan, B., Gaudreau, P., Comte, B., & Pujos-Guillot, E. (2019). Metabolites, 9(11), 250. doi: 10.3390/metabo9110250

Galactic Blog Activity

Two new entries in the past month, both related to UseGalaxy.eu..

[gProfiler is published and running on usegalaxy.eu](https://galaxyproject.eu/posts/2019/11/20/gProfiler/)

By Ivan Kuzmin. gProfiler is a toolset for functional enrichment analysis and conversions of gene lists.

gProfiler
[Great GalaxyP Tutorials hosted at GalaxyProject.eu](http://proteomicsnews.blogspot.com/2019/11/great-galaxyp-tutorials-hosted-at.html)

By Ben Orsburn. The arguments are building up for why you need this.

Galaxy P

Galaxy Platforms News

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:

[BioDivine Toolset Server](/src/use/biodivine/index.md)

Sybila

The BioDivine server hosts tools for systems biology, developed by the Systems Biology Research Centre (Sybila) in the Faculty of Informatics of Masaryk University in Brno, Czechia.

[Laniakea 2 Launched](https://laniakea-elixir-it.github.io/)

Laniakea

Version 2 of Laniakea announced at the November ELIXIR Innovation and SME Forum. Laniakea provides automatic deployment of virtual Galaxy environments. See the video for details.

[OpenRefine on Ecology Galaxy](https://ecology.usegalaxy.eu/root?tool_id=interactive_tool_openrefine)

OpenRefine in Galaxy Ecology

OpenRefine, a tool for cleaning data, is now available as an Interactive tool on Ecology Galaxy.

[UseGalaxy.*](/src/usegalaxy/index.md) News

UseGalaxy.*

Galaxy Platforms in Publications

Platforms that were referenced at least twice in the past month's publications:

25 : Huttenhower 9 : UseGalaxy.eu 8 : CPT 8 : RepeatExplorer 5 : Workflow4Metabolomics 4 : Cistrome 4 : Galaxy-P 3 : UseGalaxy.org.au 2 : ARGs-OAP 2 : Orione

And the ProteoRE group is hiring too. See below.

Doc, Hub, and Training Updates

Defining Data Types in Galaxy

New comprehensive documentation by @selten on how to define data types for Galaxy.

Guide to creating new datatypes
Cite GTN Tutorials

Thanks to Helena Rasche, every GTN Tutorial now includes a Citing this Tutorial section, including a BibTex citation for the tutorial.

Cite tutorials
Galaxy on Windows

The documentation on how to run Galaxy on Windows has been completely revamped by Tomas Klingström to use the Windows Subsystem for Linux.

Galaxy on Windows
Account Creation Help

The account creation documentation was expanded by Jennifer Hillman-Jackson to cover additional situations and help resources.

Accounts help
Metatranscriptomics analysis using microbiome RNA-seq data

By Pratik Jagtap, Subina Mehta, Ray Sajulga, Bérénice Batut, Emma Leith, Praveen Kumar

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).

ASAIM Workflow
[Galaxy 101 for everyone](https://training.galaxyproject.org/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html)

By Anne Fouilloux, Nadia Goué, Christopher Barnett, Michele Maroni, Olha Nahorna, Dave Clements, Saskia Hiltemann. Familiarize yourself with Galaxy, even if you aren't working in life sciences.

Galaxy for everyone

Who's Hiring

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.)

[Master's student position at bioinformatics core facility](https://candidate.hr-manager.net/ApplicationInit.aspx/?cid=1307&departmentId=19025&ProjectId=150840)

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.

BRIC @ University of Copenhagen
[Conception et évaluation de workflow d'analyse proteogénomique d’intérêt biomédical sous Galaxy](https://www.sfbi.fr/node/12163)

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".

ProteoRE
[Grad Students: Plant Computational Genomics](http://plantcompgenomics.com/graduate-students/)

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.

![Plant Computational Genomics at UConn ](/images/logos/uconn-plant-comp-genomics.png)
[DevOps engineer for large scale Galaxy](https://galactic-core.com/)

Take the Galaxy deployments to the next level with the core team members at Galactic Core. Email recruiting@galactic-core.com.

Galactic Core Logo
[Software engineer, system analysts / administrators, data analyst, and a community and/or research manager](https://usegalaxy-eu.github.io/posts/2019/01/10/openpositions/)

The The European Galaxy Team has open positions in Freiburg, Germany.

Galaxy Europe

Releases

Galaxy 19.09

Galaxy

The 19.09 release of Galaxy is out and full of new features:

Want the details? See the developer and admin release announcement and the user release announcement.

Other News

$3.5 million NSF grant to use GPUs in Galaxy

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.

Speeding up science
Galaxy Help Forum Turns One!

The Galaxy Help online forum turned one year old November 19. This Discourse based site now has over 3500 posts and 1000 users. Give it a look.

A banner year for help
Platypi (?) Spotted at Galaxy Africa!

Platypus!

And now, everybody wants one.

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.