April 2019 Galactic News

GCC2019 registration and abstract submission, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more!

April 3rd 2019

Galaxy News

The April 2019 Galactic News is here! This is a summary of what is going on in the Galaxy community.

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


GCC2019 Registration & Abstract Submission

We are pleased to announce that registration and abstract submission for the 2019 Galaxy Community Conference (GCC2019) are now open.

GCC2019

GCC2019 will be held 1-6 July in Freiburg, Germany. The tenth GCC will have many familiar features from earlier years, including accepted and lightning talks, posters and demos, birds-of-a-feather gatherings (BoFs), training, and a CollaborationFest. GCC2019 brings the most significant conference program update in several years:

  • some training will be integrated with the main conference,
  • three days of conference instead of two,
  • several parallel sessions,
  • and a strong emphasis on organizing content by domain.

GCC2019, like every GCC before it, will be built around community. Training topics are nominated, selected, and presented by the community. Presentations will feature the full spectrum of Galaxy applications, enhancements and deployments from the community as well.

If you are working in data intensive life science research then there will not be a better place to share your work, learn from others, and find new collaborators.

Please find additional information on GCC2019 here.

GCC2019 Sponsors

We are very pleased to welcome Limagrain as a Silver Sponsor for GCC2019.

Limagrain

Limagrain: From earth to life

As the fourth largest seed company worldwide, Limagrain’s mission is to move agriculture forward to meet global food related challenges. Limagrain is a cooperative group founded and managed by French farmers. Its parent company, Coopérative Limagrain, brings together nearly 2,000 farmers located in the center of France, in the Limagne Val d'Allier plain. The Group creates, produces and distributes field seeds, vegetable seeds and cereal products. Limagrain is present in 56 countries and has more than 10,000 employees. It makes nearly 2.5 billion Euros of sales with recognized brands on their markets: LG, Vilmorin, Hazera, Harris Moran, Jacquet, Brossard.

After participating for several years, Limagrain has the pleasure to help out with the Galaxy Community Conference organization for the first time ever. With over 200 Limagrain users worldwide and hundreds of tools dedicated to agronomic research, Galaxy has become central to Bioinformatics and Bioanalysis platforms of Limagrain research activities. By leveraging access to sequencing data of the plant species and by gathering tools and workflows tailored towards breeding, Galaxy is key to Limagrain competitiveness.

Your Organization/Vendor Here!

GCC2019 is looking for sponsors! If your organization wants to help put on the premier Galaxy event of the year, then please contact the organizers). And please encourage your vendors to consider sponsoring as well. Sponsors are potential partners for participants and their contributions make GCC affordable (and maybe even possible).

Upcoming events

These and other Galaxy related events are coming up:

DateTopic/EventVenue/LocationContact
April 2nd 2019 Genome assembly using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
April 3rd 2019 Variant detection using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
April 4th 2019 RNA Seq analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
April 5th 2019 Metagenomics analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
April 7th 2019 P38 FungiDB: Integrating genomic data for pathogens and model organisms and providing advanced search capabilities and large-scale data analysis Biocuration 2019, Cambridge, United Kingdom Training offered by GTN MemberAchchuthan Shanmugasundram
April 15th 2019 Initiation aux gestionnaires de workflow South Green (Galaxy et TOGGLe) et à l’application Gigwa IRD, Montpellier, France Training offered by GTN MemberFormateurs
April 15th 2019 Genome assembly and annotation using Galaxy National Institutes of Health (NIH), Bethesda, Maryland, United States Training offered by GTN Membermo@galaxyproject.org
April 16th 2019 Longitudinal and Context Visualization for Precision Oncology BioIT World, Boston, Massachusetts, United States Jeremy Goecks
April 23rd 2019 Elixir Galaxy Community - Workshop at Roscoff/France Station Biological De Roscoff, Roscoff, France Training offered by GTN MemberGildas Le Corguillé
April 29th 2019 de novo assembly of transcriptomes using HPC resources Indiana University, Bloomington, Indiana, United States help@ncgas.org
May 13th 2019 Science Gateways Bootcamp Indianapolis, Indiana, United States' help@sciencegateways.org.
May 17th 2019 Initiation aux analyses de données transcriptomiques IRD, Montpellier, France Training offered by GTN MemberFormateurs
May 23rd 2019 Initiation aux analyses de données metabarcoding IRD, Montpellier, France Training offered by GTN MemberFormateurs
July 1st 2019 2019 Galaxy Community Conference (GCC2019) Freiburg, Germany Training offered by GTN MemberOrganizers

Publications

120 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in March.

Highlighted Publications

Recently added Galactic and Stellar publications:

Three of the four highlighted publications are open access.

Publication Topics

# Tag # Tag # Tag # Tag
83 +Methods 27 +UsePublic 16 +UseMain 14 +Workbench
11 +UseLocal 10 +RefPublic 6 +Reproducibility 5 +IsGalaxy
3 +Tools 1 +Cloud 1 +Other 1 +Shared
1 +Visualization

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. A lot was added in March:

graphclust

GraphClust

The GraphClust2 server is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow.

Language Analysis Portal

The language analysis portal (LAP) provides an intuitive and easy-to-use web interface to a centralized repository of a wide range of language technology tools, all installed on a high-performance computing (HPC) cluster. Users are able to compose and run workflows using an in-browser graphical interface, with multiple tools and resources chained together in potentially complex pipelines. Although the project reaches out to a diverse set of user groups, it particularly aims to facilitate use of language analysis in the social sciences, humanities, and other fields without strong computational traditions.

CAFU

cafu

CAFU is a Galaxy-based bioinformatics framework for comprehensive assembly and functional annotation of unmapped RNA-seq data from single- and mixed-species samples which integrates plenty of existing NGS analytical tools and our developed programs, and features an easy-to-use interface to manage, manipulate and most importantly, explore large-scale unmapped reads.

Galaxy Platforms in Publications

We tag papers that use, mention, implement or extend public Galaxy platforms (servers, services, clouds, containers...). Here are the counts for the past month's publications:

# Tag # Tag # Tag # Tag
11 >Huttenhower 5 >Workflow4Metabolomics 4 >ARGs-OAP 4 >RepeatExplorer
2 >Langille 2 >UseGalaxy.eu 1 >AmrPlusPlus 1 >ARIES
1 >CAFU 1 >Cistrome 1 >CPT 1 >EGI
1 >Galaxy-P 1 >Genomic Hyperbrowser 1 >GraphClust 1 >MPDSDM
1 >MPDSTB 1 >Pasteur 1 >PreSTIGE 1 >ProteoRE
1 >RNA Workbench 1 >SouthGreen

Galactic Blog

New Galactic Blog Post

This month we have a Galactic Blog post where Björn Grüning gives a sneak peak at GCC2019.


Who's Hiring

Please Help! Yes you!

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.


Doc, Hub, and Training Updates

Updates from the Galaxy Training Materials in March:

GTN Training Materials

Galaxy Training Materials


ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in March 2019.

Releases

New additions to the Galaxy Ecosystem.

CloudBridge 2.0 release

CloudBridge is a Python library that offers a uniform interface to major Infrastructure-as-a-Service (IaaS) cloud providers. CloudBridge ensures operational consistency across the supported providers allowing the same code to run consistently across multiple cloud providers. With this release, CloudBridge supports Amazon Web Service (AWS), Microsoft Azure, OpenStack, and now Goodle cloud. This release is further characterized by improved code consistency.

Please see the release notes for additional information.

Galaxy Status

We are happy to announce that we now have a status page to monitor the status of our public useGalaxy.* servers and certain Galaxy services. This page tracks the operational status of usegalaxy.org, usegalaxy.eu, and usegalaxy.org.au servers, as well as Galaxy services including the Galaxy (Main) Tool Shed, Galaxy CloudLaunch, and Galaxy test services. Status.galaxyproject.org will serve as the central channel for announcing and tracking planned downtime and routine maintenance.

galaxy-lib 19.5.1

galaxy-lib is a subset of the Galaxy core code base designed to be used as a library. This subset has minimal dependencies and should be Python 3 compatible. It's available from GitHub and PyPi.


Other News