August 2019 Galactic News
GCC2019 is done; BCC2020 is coming
The August 2019 Galactic News is here!
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Events: GCC2019 is done; BCC2020 is coming! Galaxy ♥ BioHackathon Europe!
- Plus deadlines this month and 19 other events in the next 90 days.
- 178 new publications, including 5 highlighted ones.
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- Getting the most out of 1) Galaxy on Twitter, and 2) Pan-Galactic Search
- Galaxy Platform News from UseGalaxy.* and the Human Cell Atlas.
- Seven Open positions in four countries on two continents.
- Updates to training materials and documentation.
- New releases.
If you have anything to include to next month's newsletter, then please send it to outreach@galaxyproject.org.
Events
](/src/events/gcc2019/index.md)
The 2019 Galaxy Community Conference is done! GCC2019 was held 1-8 July, in Freiburg, Germany, the home of Galaxy Europe. It was a smashing success by any measure:
- 231 total participants
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65 Talks
- 54 Posters and 14 Demos
- 39 Training Sessions
- ~30 Birds of a Feather meetups
The slides for most talks and posters are online. Videos of selected trainings and most talks will be posted (we hope) in August.
Many, many thanks to all the instructors, presenters, scientific committee members, and BOF, conference and CoFest organizers for making 2019 such an excellent year.
We are pleased to announce that the 2020 Galaxy Community Conference will be held jointly with the 2020 Bioinformatics Open Source Conference (BOSC), at the Bioinformatics Community Conference (BCC2020).
The new name, BCC2020, reflects the increased blending of these two communities that is happening at next year's event. BCC2020 will feature more theme/domain driven presentation, poster and demo sessions, featuring content from both communities.
BCC2020 will be held July 18-25, at Victoria University, on the University of Toronto campus, in Toronto, Ontario, Canada, immediately after ISMB 2020 ends in Montreal. BCC2020 will be hosted by the Ontario Institute for Cancer Research (OICR) and the University of Toronto.
BCC2020 will feature a similar mix of training, conference, and CollaborationFest, that GCCBOSC2018 did.
Galaxy will be featured at BioHackathon-Europe 2019 as a prominent part of many of this year's selected projects:
- Interoperable Workflows for Communities
- Improve the support of Common Workflow Language in Galaxy
- Towards seamless Galaxy and InterMine integration: Enhanced region analysis
- Scalable delivery of FAIR training in Life Sciences using Galaxy and the Carpentries training material
- Development of a Pulsar toolkit
- Updating the Galaksio workflow management interface for Galaxy and migrating it to Vue.js
- A graph database of Galaxy tool interoperability
- Bioconda and Biocontainers helpdesk
Join us to learn from and work with experts of the Open Source Life Science community, and discuss the future of the ELIXIR Galaxy community and enjoy the great food and venue.
Interested? Registration is available on a first come, first serve basis. Registration is free, but space is limited. Register now.
Deadlines this month
- Reproducible and Transparent Genomic Analysis with Galaxy, ASHG 2019, Houston, Texas, United States. Early registration: August 20.
- NGS data analysis with Galaxy for clinical applications, GMDS-Jahrestagung, Dortmund, Germany. Advance registration: August 30.
All Upcoming events
There is a lot going on in the next 3 months.
Publications
178 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in the last month, pushing the total number of publications past 8,000.
There were 5 Galactic and Stellar publications added, and 4 of them are open access:
Delfina Malandrino, Ilaria Manno, Alberto Negro, Andrea Petta, Luigi Serra, Concita Cantarella & Vittorio Scarano. Source Code for Biology and Medicine volume 14, Article number: 4 (2019) doi: 10.1186/s13029-019-0074-4
Veronika Kapustová, Zuzana Tulpová, Helena Toegelová, Petr Novák, Jiří Macas, Miroslava Karafiátová, Eva Hřibová, Jaroslav Doležel and Hana Šimková. Int. J. Mol. Sci. 2019, 20(10), 2483; doi: 10.3390/ijms20102483
Jin Wang, Bing Liang Alvin Chew, Yong Lai, Hongping Dong, Luang Xu, Seetharamsingh Balamkundu, Weiling Maggie Cai, Liang Cui, Chuan Fa Liu, Xin-Yuan Fu, Zhenguo Lin, Pei-Yong Shi, Timothy K. Lu, Dahai Luo, Samie R. Jaffrey, Peter C. Dedon. bioRxiv doi: 10.1101/683045
Caleb W. Easterly, Ray Sajulga, Subina Mehta, James Johnson, Praveen Kumar, Shane Hubler, Bart Mesuere, Joel Rudney, Timothy J. Griffin and Pratik D Jagtap. Molecular & Cellular Proteomics June 24, 2019, mcp.RA118.001240; doi: 10.1074/mcp.RA118.001240
Publication Topics
| # | Tag | # | Tag | # | Tag | # | Tag | |||
|---|---|---|---|---|---|---|---|---|---|---|
| 127 | +Methods | 50 | +UsePublic | 24 | +Workbench | 17 | +UseMain | |||
| 16 | +UseLocal | 11 | +RefPublic | 8 | +Reproducibility | 2 | +IsGalaxy | |||
| 2 | +Shared | 2 | +Tools | 1 | +Cloud | 1 | +HowTo | |||
| 1 | +Other | 1 | +Unknown |
Galactic Blog Activity
An update from the team behind @galaxyproject tweets, motivated by the new @gxytraining account.
There a lot more going on than @galaxyproject and #UseGalaxy.
How to find Galaxy info on the web, and find only Galaxy info on the web. No more phones, astronomy, soccer, cars, chocolate, or Ansible (OK, maybe Ansible).
Also answers the question of "Where do cars go after they die?"
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.
- UseGalaxy.eu hits 7000 users and 10.000.000 datasets.
- UseGalaxy.org and UseGalaxy.org.au now have the Galaxy Training Network tutorial datasets. And they are all automatically updated too, courtesy of Helena Rasche. (And, ahem, UseGalaxy.eu has had this data forever.)
The newly launched Human Cell Atlas Galaxy instance has tools and workflows for the analysis of Single Cell RNA-Seq data. It includes a module that connects to the Matrix Service API of the Human Cell Atlas’s Data Coordination Platform that enables retrieval of gene expression matrices from any data sets in the Human Cell Atlas. This server is hosted by the UseGalaxy.eu team.
Galaxy Platforms in Publications
Platforms that were referenced at least twice in the past month's publications:
| # | Platform | # | Platform | # | Platform | # | Platform | |||
|---|---|---|---|---|---|---|---|---|---|---|
| 19 | >Huttenhower | 7 | >CPT | 6 | >RepeatExplorer | 5 | >Workflow4Metabolomics | |||
| 4 | >Galaxy-P | 2 | >Cistrome | 2 | >deepTools | 2 | [>Globus Genomics](https://www.zotero.org/groups/1732893/galaxy/tags/>Globus Genomics) | |||
| 2 | >RiboGalaxy | 2 | >UseGalaxy.eu |
Who's Hiring
The dark energy of irreproducible research is threatening the science universe! Please help the Galaxy push it back! Have a Galaxy-related opening? Send it to outreach @ galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.
AbSci, Vancouver, Washington, United States
Wageningen University & Research is hiring.
In the Blankenberg Lab at the Cleveland Clinic, Cleveland, Ohio, United States.
At the VIB-UGent Center for Plant Systems Biology, with ELIXIR Belgium.
At the VIB-UGent Center for Plant Systems Biology, with ELIXIR Belgium.
At the VIB-UGent Center for Plant Systems Biology, with ELIXIR Belgium.
The The European Galaxy Team has open positions in Freiburg, Germany.
Doc, Hub, and Training Updates
By [Delphine Lariviere](https://training.galaxyproject.org/training-material/hall-of-fame#delphine-l) and [Bérénice Batut](https://training.galaxyproject.org/training-material/hall-of-fame#bebatut).
Identification of essential prokaryotic genes using Transposon insertion sequencing in Galaxy.
By [Pablo Moreno](https://training.galaxyproject.org/training-material/hall-of-fame#pcm32), [Enis Afgan](https://training.galaxyproject.org/training-material/hall-of-fame#afgane), [Nuwan Goonasekera](https://training.galaxyproject.org/training-material/hall-of-fame#nuwang), [Alex Mahmoud](https://training.galaxyproject.org/training-material/hall-of-fame#almahmoud), [Sergey Golitsynskiy](https://training.galaxyproject.org/training-material/hall-of-fame#ic4f).
A uniform way to install a production-grade Galaxy with a single command in a variety of environments.
Updated by [Nate Coraor](https://training.galaxyproject.org/training-material/hall-of-fame#natefoo), [Nicola Soranzo](https://training.galaxyproject.org/training-material/hall-of-fame#nsoranzo), [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame#erasche), and all of the awesome participants at GCC2019 who provided valuable feedback and great questions during [the first day of training](https://gcc2019.sched.com/type/a.+training/admin+%2F+dev)!
Galaxy can now [access](https://github.com/galaxyproject/cloudauthz#cloudauthz) Google Cloud Storage, (joining AWS and Azure). This builds on Google Cloud Platform support in new release of CloudAuthz.
By [Mélanie Petera](https://training.galaxyproject.org/training-material/hall-of-fame#melpetera), [Gildas Le Corguillé](https://training.galaxyproject.org/training-material/hall-of-fame#lecorguille), [Jean-François Martin](https://training.galaxyproject.org/training-material/hall-of-fame#jfrancoismartin), [Yann Guitton](https://training.galaxyproject.org/training-material/hall-of-fame#yguitton), [Workflow4Metabolomics core team](https://training.galaxyproject.org/training-material/hall-of-fame#workflow4metabolomics)
How to conduct metabolomic data analysis from preprocessing to annotation using Galaxy.
Monitoring is an incredibly important part of server maintenance. Being able to observe trends and identify hot spots by collecting metrics gives you the ability to respond to issues that arise in production. Updated by [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame#erasche) to include additional details.
The [Admin topic tutorials (31 of them!)](https://training.galaxyproject.org/training-material/topics/admin/) are now organised into subtopics to make it easier to know where to start. This feature is generically available and will be expanded other topics in the future to help users find content that is important to them. Thanks to [Saskia Hiltemann](https://training.galaxyproject.org/training-material/hall-of-fame#shiltemann) and [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame#erasche).
There is now a search box in each topic, to help find what you are looking for. Thanks again to, you guessed it, [Saskia Hiltemann](https://training.galaxyproject.org/training-material/hall-of-fame#shiltemann) and [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame#erasche).
Releases
New additions (and editions) in the Galaxy Ecosystem.
[Planemo](https://pypi.python.org/pypi/planemo) is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included [numerous fixes and enhancements](https://github.com/galaxyproject/planemo/blob/master/HISTORY.rst). See [GitHub for details](https://github.com/galaxyproject/planemo/blob/master/HISTORY.rst).
Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows. It has extensive documentation. This release features numerous newly contributed features.