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September 2019 Galactic News

Events! Pubs! Platforms! Jobs! Doc! Tutorials! Releases! And some other news too.

Galaxy News

The September 2019 Galactic News continues 1) the reformatting that started last month, and 2) the fine tradition of including all Galactic news under this or any other sun:

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


Galaxy @ INCOB
Galaxy @ INCOB

Galaxy, and especially the Galaxy Australia community will have a strong presence at INCOB 2019 in Jakarta. There will be an Introduction to Galaxy workshop and a conference talk about the Galaxy Australia platform.

In addition, we will also be taking first steps towards a regional Galaxy community and platform for the INCOB community. Interested? We hope to see you in Jakarta.

You wrote it, now get it used: Publishing your software with Galaxy and Bioconda
Publishing your software with Galaxy and Bioconda

Learn how to increase the ease with which others can install and use your bioinformatics software.

This workshop at ACM BCB, on September 7, in Niagara Falls, New York will show participants how to use two technologies that make it easy for researchers to deploy and use your software: The Galaxy ToolShed, and Bioconda. Space is limited and registration is required.

GalaxyAfrica 2019
Galaxy Africa 2019

GalaxyAfrica 2019 will be 14-15 November, in collaboration with the ASBCB/ISCB Africa conference in Kumasi, Ghana. We will offer Galaxy training for researchers, and training for systems administrators who need to maintain a local installation. This year we are calling for abstracts for three oral presentations that demonstrate the use of Galaxy in your research projects.

Upcoming Events
Upcoming Events

There are

  • 30 upcoming events
  • on 4 continents (plus online)
  • in Sri Lanka, Ireland, US, Germany, Indonesia, Japan, UK, Belgium, Australia, the Netherlands, and France
  • on installing Galaxy, getting your tools used, clinical applications, expanding the Galaxy and Bioconda ecosystems, microscopy image analysis, QC, assembly, RNA-Seq, variant detection, metagenomics, ...
Galaxy Training Network day - (online) CoFest and community call

The Galaxy Training Network organizes one day, every three months, for collaborative work on the training materials and calls with the community.

The next day will be on the 12th of September. Anyone who would like to contribute, learn how to contribute to the Galaxy Training Material or just catch up with the community is very welcome to join. See the event page for details.

Galaxy @ QFAB in September
Galaxy Training @ QFAB

QFAB Training is offering 5 training topics in 5 days at the end of September:

All training is offered at the Translational Research Institute (TRI) in Woolloongabba, Queensland, Australia

Galaxy Netherlands
GalaxyNL Face2Face Meeting

This year's Galaxy Netherlands Face2Face meeting will take place at:

  • Time: October 3, 13:30-16:00, with drinks afterwards
  • Location: GROW room, DTL offices, JIM 6th floor, Jaarbeursplein 6, 3521 AL Utrecht

Interested? Please register for the meeting.

Please let Saskia Hiltemann know if you have any agenda items you would like to raise for discussion, or if you would like to present any Galaxy-related work/plans you have.

[Bioconda Collaboration Fest](https://galaxyproject.eu/event/2019-08-19-bioconda-cofest/)

A collaboration fest will be held in Freiburg and elsewhere on 30 September through 1 October for Bioconda and its ecosystem. This CoFest is organised globally and decentralised. Feel free to join us in Freiburg, join other events or organise your own local Bioconda Collaboration Fest.

Deadlines this month

There are several registration deadlines this month:


150 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in the last month. There were two Galactic and Stellar publications added.

[Targeting a highly repeated germline DNA sequence for improved real-time PCR-based detection of Ascaris infection in human stool](https://doi.org/10.1371/journal.pntd.0007593)

Nils Pilotte, Jacqueline R. M. A. Maasch, Alice V. Easton, Eric Dahlstrom, Thomas B. Nutman, Steven A. Williams. PLOS Neglected Tropical Diseases 13(7): e0007593. doi: 10.1371/journal.pntd.0007593

[Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms](https://doi.org/10.1093/database/baz086)

Jochen T Bick, Shuqin Zeng, Mark D Robinson, Susanne E Ulbrich, Stefan Bauersachs. Database, Volume 2019, 2019, baz086, doi: 10.1093/database/baz086

Publication Topics

Publications are tagged with how they use, extend or reference Galaxy. The past month's pubs were tagged as:

103 : Methods 45 : UsePublic 17 : Workbench 16 : RefPublic 12 : UseMain 8 : Reproducibility 7 : UseLocal 4 : Tools 1 : Cloud

Galactic Blog Activity

The Galaxy Genome Annotation Project
[The Galaxy Genome Annotation Project](https://galaxyproject.eu/posts/2019/08/05/gga/)

The Galaxy Genome Annotation (GGA) Project is focused on supporting genome annotation inside Galaxy. This blog post by Björn Grüning highlights a few of the recent developments and the new Genome Annotation subsection of the European Galaxy server.

Galaxy Community Conference Summary
[Galaxy Community Conference Summary](https://galaxyproject.eu/posts/2019/08/06/gcc/)

A summary of the 2019 Galaxy Community Conference by Anika Erxleben, Helena Rasche, and Björn Grüning.

Slamdunk - SLAMseq analysis for nucleotide-conversion sequencing datasets
[Slamdunk - SLAMseq analysis for nucleotide-conversion sequencing datasets](https://galaxyproject.eu/posts/2019/08/06/gcc/)

This post by Tobias Neumann describes SlamDunk, a novel and fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis, that is now available on UseGalaxy.eu.

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.

[Climate Science Workbench](/src/use/climate-science-workbench/index.md)

Climate Science Workbench

Features a comprehensive set of analysis tools and consolidated workflows for climate science data analysis and visualization. This server supports general GIS data handling tools and climate analysis-specific tools. It is hosted by by the UesGalaxy.eu team. This work was presented at GCC2019 by Anne Fouilloux.

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


Galaxy Platforms in Publications

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

17 : Huttenhower 4 : CPT 4 : Workflow4Metabolomics 3 : ARGs-OAP 3 : RepeatExplorer 3 : RiboGalaxy 2 : Cistrome 2 : DDBJ 2 : GVL-Unspecified 2 : Palfinder 2 : Pasteur

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.

[Five permanent positions in bioinformatics / biostatistics](https://c3bi.pasteur.fr/four-permanent-positions-in-bioinformatics-biostatistics-m-f-at-the-institut-pasteur-paris/)

Five permanent positions in bioinformatics / biostatistics (M/F) are open at the Institut Pasteur (Paris)

![Institut Pasteur](/images/logos/InstitutePasteurLogoTrans.png)
[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)
[Bioinformatics Developer, Scientific Computing and Bioinformatics](https://absci.bamboohr.com/jobs/view.php?id=32)

AbSci, Vancouver, Washington, United States

[ELIXIR Software developer data management tools](https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/17168/software-developer-data-management-tools)

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

[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
[Application Support / Software Developer](http://jobs.unimelb.edu.au/caw/en/job/900700/application-support-software-developer)

Contribute to the operation, support and functionality developments of Galaxy Australia, an award-winning publicly available platform for performing bioinformatics analyses and workflows for Australian researchers.

Galaxy Australia

Doc, Hub, and Training Updates

[Introduction to image analysis using Galaxy](https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/tutorial.html)
Image analysis in Galaxy

By [Thomas Wollman](https://github.com/thomaswollmann)

How to segment and extract features from cell nuclei Galaxy for image analysis.

[Analyse HeLa fluorescence siRNA screen](https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html)
Viz segmentation

By [Thomas Wollman](https://github.com/thomaswollmann) and [Saskia Hiltemann](https://training.galaxyproject.org/training-material/topics/instructors/philosophies/#shiltemann)

How to use Galaxy to perform basic image analysis tasks such as format conversion, image enhancement, segmentation, and feature extraction.

[Automation with Jenkins](https://training.galaxyproject.org/training-material/topics/admin/tutorials/jenkins/tutorial.html)
Jenkins security

By [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame#erasche)

Continuous integration with Jenkins to make your Galaxy admin life easier.

[Help for Differential Expression Analysis](/src/support/diff-expression/index.md)

By [Jennifer Hillman-Jackson](/src/people/jennifer-jackson/index.md)

A new support page for one of Galaxy's most popular applications: differential gene expression analysis.

[Displaying Datasets at External Display Applications / Websites using GEDAs](/src/admin/tools/external-display-applications-tutorial/index.md)
GEDA example config

By [Dan Blankenberg](/src/people/dan/index.md)

How to add a new external display application (UCSC genome browser, GeneTrack, JBrowse, etc. to Galaxy.

[TIaaS Upgrades](https://galaxyproject.eu/tiaas.html)


[Training Infrastructure as a Service (TIaaS)](https://galaxyproject.eu/tiaas.html) is just one service that the European UseGalaxy project is providing. TIaaS got a lot of updates this summer thanks to [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame#erasche). [Read more about it](https://galaxyproject.eu/tiaas.html).


New additions (and editions) in the Galaxy Ecosystem.

BioBlend v 0.13.0

BioBlend is a Python library for interacting with CloudMan and the Galaxy API. Conceptually, it makes it possible to

  • to run analyses on Galaxy using a programmatic interface.
  • script and automate the process of cloud infrastructure provisioning and scaling via CloudMan.

See the v 0.13.0 release notes for more.

Other News