August 2019 Galactic News

GCC2019 is done; BCC2020 is coming

August 1st 2019

The August 2019 Galactic News is here!

Galaxy News

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

Events

GCC2019
GCC2019: Biggest GCC Yet

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:

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.

BCC2020
BCC2020: July 18-25, 2020, Toronto

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.

BCC2020
Galaxy @ BioHackathon-Europe 2019

Galaxy will be featured at BioHackathon-Europe 2019 as a prominent part of many of this year's selected projects:

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

All Upcoming events

There is a lot going on in the next 3 months.

DateTopic/EventVenue/LocationContact
August 1st 2019 "Teaching undergraduate genomics with Galaxy” and “Resources and recommendations for teaching undergraduate genomics with Galaxy" ASMCUE 2019, Tyson, Virginia, United States Training offered by GTN MemberMo Heydarian, Anton Nekrutenko
August 1st 2019 Variant detection using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
August 2nd 2019 Metagenomics analysis using Galaxy Translational Research Institute (TRI), Woolloongabba, Queensland, Australia Training offered by GTN Membertraining@qfab.org
September 7th 2019 You wrote it, now get it used: Publishing your software with Galaxy and Bioconda ACM BCB, Niagara Falls, New York, United States Training offered by GTN MemberDan Blankenberg, Martin Čech
September 8th 2019 NGS data analysis with Galaxy for clinical applications GMDS-Jahrestagung, Dortmund, Germany Training offered by GTN MemberMarkus Wolfien
September 9th 2019 Gateways Focus Week Chicago, Illinois, United States help @ sciencegateways.org
September 16th 2019 UseGalaxy.be: platform for data-intensive research ELIXIR Belgium All Hands Meeting 2019, Brussels, Belgium Frederik Coppens
September 23rd 2019 NGS Platforms: how data generation impacts bioinformatics analysis - quality control QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
September 23rd 2019 Galaxy @ Gateways 2019 Gateways 2019, San Diego, California, United States James Taylor, Dave Clements
September 24th 2019 Genome assembly using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
September 25th 2019 RNA Seq analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
September 26th 2019 Variant detection using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
September 27th 2019 Metagenomics analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
October 3rd 2019 GalaxyNL Face2Face Meeting Utrecht, the Netherlands Saskia Hiltemann
October 8th 2019 Using Galaxy for RNA-seq VIB, Ghent, Belgium Lieven Sterck, Tuur Muyldermans
October 10th 2019 Reproducible Genomic Data Analysis with the Galaxy Workbench AISES 2019, Milwaukee, Wisconsin, United States Training offered by GTN MemberMo Heydarian, Dave Clements
October 14th 2019 Reproducible and Transparent Genomic Analysis with Galaxy ASHG 2019, Houston, Texas, United States Training offered by GTN MemberJeremy Goecks, Mo Heydarian
October 29th 2019 Analyse avancée de séquences Bordeaux, France Training offered by GTN MemberMacha Nikolski
October 30th 2019 Genomic data science with the Galaxy workbench 2019 SACNAS, Honolulu, Hawai'i, United States Training offered by GTN MemberMo Heydarian, Dave Clements
November 18th 2019 Galaxy @ BioHackathon-Europe 2019 Campus des Berges de Seine, Paris, France Project organizers

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

Galaxy on Twitter

An update from the team behind @galaxyproject tweets, motivated by the new @gxytraining account.

There a lot more going on than @galaxyproject and #UseGalaxy.

Where do cars go after they die?

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.*

Human Cell Atlas gets a Galaxy

Human Cell Atlas

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
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.

Wageningen University & Research is hiring.

Wageningen University & Research

In the Blankenberg Lab at the Cleveland Clinic, Cleveland, Ohio, United States.

Cleveland Clinic

At the VIB-UGent Center for Plant Systems Biology, with ELIXIR Belgium.

VIB

At the VIB-UGent Center for Plant Systems Biology, with ELIXIR Belgium.

VIB

At the VIB-UGent Center for Plant Systems Biology, with ELIXIR Belgium.

VIB

Doc, Hub, and Training Updates

normalisation

By Delphine Lariviere and Bérénice Batut.

Identification of essential prokaryotic genes using Transposon insertion sequencing in Galaxy.

2 New Tutorials for Galaxy on Kubernetes: Deploying Galaxy and Managing Galaxy
Kubernetes

By Pablo Moreno, Enis Afgan, Nuwan Goonasekera, Alex Mahmoud, Sergey Golitsynskiy.

A uniform way to install a production-grade Galaxy with a single command in a variety of environments.

Example configuration from tutorial

Updated by Nate Coraor, Nicola Soranzo, Helena Rasche, and all of the awesome participants at GCC2019 who provided valuable feedback and great questions during the first day of training!

Google Cloud Platform

Galaxy can now access Google Cloud Storage, (joining AWS and Azure). This builds on Google Cloud Platform support in new release of CloudAuthz.

normalisation

By Mélanie Petera, Gildas Le Corguillé, Jean-François Martin, Yann Guitton, Workflow4Metabolomics core team

How to conduct metabolomic data analysis from preprocessing to annotation using Galaxy.

GTN Tweets!

Galaxy Training Materials The Galaxy Training Network now has a Twitter account! Follow @GxyTraining to stay up to date on GTN training materials, events, and announcements!

Hands-on: Add a second query to an existing graph

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 to include additional details.

GTN Infrastructure: Subtopics
Subtopics in the Training material

The Admin topic tutorials (31 of them!) 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 and Helena Rasche.

GTN Infrastructure: Search
Search feature in the Training material

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 and Helena Rasche.

Releases

New additions (and editions) in the Galaxy Ecosystem.

Planemo 0.61.0
Planemo

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included numerous fixes and enhancements. See GitHub for details.

Ephemeris v 0.10.3

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.