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October 2019 Galactic News

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

Galaxy News

The October 2019 Galactic News includes 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.


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.

Early registration ends 20 October.

Galaxy Netherlands
[GalaxyNL Face2Face Meeting](/events/2019-10-galaxynl/)

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.

[Workflow4Experimenters international course (W4E2020)](https://workflow4metabolomics.org/w4e2020)

Brussels, Belgium. Monday 3th to Friday February 7th 2020.

This one-week course (entirely in English), Learn to use the W4M infrastructure and analyze your own LC-MS, GC-MS, or NMR data. Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring.

Preregister by 3 November.

Upcoming Events
Upcoming Events

There are

  • 20 upcoming events
  • on 5 continents
  • in Italy, Germany, the Netherlands, Greece, Estonia, Belgium, US, France, Taiwan, Ghana, Australia, and UK.
  • on RNA-Seq, bisulfite sequencing, reproducibility, CWL, cancer, single cell, metabarcoding, and metabolomics!
[Galaxy for linking bisulfite sequencing with RNA sequencing](https://www.denbi.de/training/663-galaxy-for-linking-bisulfite-sequencing-with-rna-sequencing)

Galaxy, differential gene expression analysis, bisulfite sequencing analysis, and Nanopore data exploration and usage. Three days in Freiburg starting 9 October.

Galaxy @ AISES
[Galaxy @ AISES 2019](/events/2019-10-aises/)

Reproducible Genomic Data Analysis with the Galaxy Workbench, 9:30 - 11:20, Friday, October 11.

Galaxy @ ASHG
[Galaxy @ ASHG 2019](http://www.ashg.org/2019meeting/asp/soe/webroot/soe.shtml#?search=galaxy)

Reproducible and Transparent Genomic Analysis with Galaxy, Tuesday, October 15, 1:30 - 3:00. Register now, as space is limited.

Analyse avancée de séquences
[Analyse avancée de séquences](https://cnrsformation.cnrs.fr/stage-19019-Analyse-avancee-de-sequences.html?axe=98)

Savoir utiliser l'environnement Galaxy, à partir du 29 octobre.

Deadlines this month

There are several registration deadlines this month:


143 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in the last month. There were 9 Galactic and Stellar publications added, and four of those are open access:

[BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows](https://www.nature.com/articles/s41597-019-0177-4)

Andrio, Pau, Adam Hospital, et al. 2019. Scientific Data 6 (1): 1–8. doi: 10.1038/s41597-019-0177-4.

[Understanding rumen function using (meta)genome-guided metaproteomics](https://nmbu.brage.unit.no/nmbu-xmlui/handle/11250/2609080)

Andersen, Thea Os. 2019. Thesis, Norwegian University of Life Sciences.

[Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges](https://doi.org/10.1186/s13059-019-1794-0)

Ellrott, Kyle, Alex Buchanan, et al. Genome Biology 20 (1): 195. doi: 10.1186/s13059-019-1794-0. 2019.

[You Wrote It, Now Get It Used: Publishing Your Software with Galaxy and Bioconda](http://doi.acm.org/10.1145/3307339.3343178)

Daniel Blankenberg, Martin Cech. 2019. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB '19). ACM, New York, NY, USA, 559-559. DOI: 10.1145/3307339.3343178

Publication Topics

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

104 : Methods 46 : UsePublic 15 : Workbench 12 : UseLocal 11 : UseMain 8 : Tools 7 : RefPublic 4 : IsGalaxy 2 : Cloud 2 : Other 2 : Project 2 : Reproducibility 1 : HowTo

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 were are many new platforms this month:



The Inter-Domain Ecological Network Analysis Pipeline (IDENAP) server models, analyzes and manages the Inter-Domain Ecological Networks (IDENs) from metagenomic datasets, e.g. GeoChip and Sequencing, and synchronous plant surveys.

[ELIXIR Belgium Galaxy](/use/usegalaxy-be/)


The ELIXIR Belgium Galaxy server has been launched. This server focuses on serving researchers in Belgium, provides a wealth of tools, and reference data for plant species from the PLAZA data warehouse.

[Lebanese University Galaxy](/use/lebanese-university/)

Lebanese University Galaxy

Lebanese University has launched the first public Galaxy server in the Middle East. The server features the SpCLUST tool set for fast and reliable clustering of potentially divergent biological sequences. It also supports the CD-Hit and DNAClust tool sets.


NG-Tax workflow

The NG-Tax server provides a semantic framework for high-throughput marker gene (amplicon) analysis. The server requires that you create a login, but anyone can create a login. Supports both NG-Tax versions 1 & 2.

[Galaxy for Ecology](/use/ecology/)

Galaxy for Ecology: Mapped prediction

Galaxy for Ecology is a web platform to get, process, analyze and visualize ecological data, including species occurrence data, protocoled data from Vigie-Nature, and climatic data from Worldclim.

Galaxy Platforms in Publications

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

23 : Huttenhower 5 : Workflow4Metabolomics 4 : ARGs-OAP 4 : UseGalaxy.eu 3 : Cistrome 3 : Pasteur 2 : AmrPlusPlus 2 : RepeatExplorer 2 : UseGalaxy.org.au

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.

[Specialist, Bioinformatician](https://jobs.gsk.com/en-gb/jobs/226415)

Full-Time, Rixensart, Belgium.

Develop core bioinformatics pipelines using a variety of environments (incl. Linux, Galaxy, DNA-Nexus) for base-calling, demultiplexing, data quality control, sequence alignment, variant calling, quantifying gene expression...

GSK Logo
[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

[Galaxy-focused opportunity with core team members](https://galactic-core.com/)

Interested in an exciting new Galaxy-focused opportunity with core team members? Contact recruiting@galactic-core.com today.

Galactic Core Logo
[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

Doc, Hub, and Training Updates

[Reference-based RNA-Seq data analysis](https://training.galaxyproject.org/topics/transcriptomics/tutorials/ref-based/tutorial.html)
Slice of overall workflow

The [Reference-based RNA-Seq data analysis](https://training.galaxyproject.org/topics/transcriptomics/tutorials/ref-based/tutorial.html) has been expanded by [Bérénice Batut](https://training.galaxyproject.org/training-material/hall-of-fame#bebatut), [Anika Erxleben](https://training.galaxyproject.org/training-material/hall-of-fame#erxleben), and [Nicola Soranzo](https://training.galaxyproject.org/training-material/hall-of-fame#nsoranzo) to provide more details about DGE, GO and KEGG analysis, and visualization.

[EWAS data analysis of 450k data](https://training.galaxyproject.org/topics/epigenetics/tutorials/ewas-suite/tutorial.html)
Visualizing results at UCSC

By [Katarzyna Murat](https://training.galaxyproject.org/training-material/hall-of-fame#kpbioteam) and [Krzysztof Poterlowicz](https://training.galaxyproject.org/training-material/hall-of-fame#kpoterlowicz)

This tutorial identifies differentially methylated regions and positions associated with treatment resistant melanomas.

[Quality Control](https://training.galaxyproject.org/topics/sequence-analysis/tutorials/quality-control/tutorial.html)
Quality Score Encoding

The [Quality Control tutorial](https://training.galaxyproject.org/topics/sequence-analysis/tutorials/quality-control/tutorial.html) has been updated by [Bérénice Batut](https://training.galaxyproject.org/training-material/hall-of-fame#bebatut), [Saskia Hiltemann](https://shiltemann.github.io/), [Anup Kumar](https://github.com/anuprulez), Matthias (which one, we ask?) and [Anika Erxleben](https://github.com/erxleben). It provides more details about FastQC reports and clarifies the trimming approach and paired-end explanation.

Chat support in [Admin](https://training.galaxyproject.org/training-material/topics/admin/) & [Dev](https://training.galaxyproject.org/training-material/topics/dev/) tutorials
Start Chatting

[Galaxy Admin](https://training.galaxyproject.org/training-material/topics/admin/) & [Dev](https://training.galaxyproject.org/training-material/topics/dev/) topics now include Gitter chat rooms embedded into the tutorials. Ask your questions or just start a discussion about the training topics with fellow learners and tutorial authors.

[Annotating a protein list identified by LC-MS/MS experiments](https://training.galaxyproject.org/topics/proteomics/tutorials/proteome_annotation/tutorial.html)
Slice of overall workflow

By [Valentin Loux](https://training.galaxyproject.org/training-material/hall-of-fame#vloux), [Florence Combes](https://training.galaxyproject.org/training-material/hall-of-fame#combesf), [David Christiany](https://training.galaxyproject.org/training-material/hall-of-fame#davidchristiany), [Yves Vandenbrouck](https://training.galaxyproject.org/training-material/hall-of-fame#yvandenb).

Annotate a protein list identified by LC-MS/MS experiments using the [ProteoRE Galaxy instance](http://www.proteore.org/).

[Pre-processing of 10X Single-Cell RNA Datasets](https://training.galaxyproject.org/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial.html)
CelSeq and 10x

By [Mehmet Tekman](https://training.galaxyproject.org/training-material/hall-of-fame#mtekman), [Hans-Rudolf Hotz](https://training.galaxyproject.org/training-material/hall-of-fame#hrhotz), and [Daniel Blankenberg](https://training.galaxyproject.org/training-material/hall-of-fame#blankenberg)

Map and quantify scRNA-seq FASTQ data via RNA STARsolo, and reproduce a Cell Ranger workflow using the DropletUtils suite. Explore the use of barcode rankings to determine better filtering thresholds to generate a high quality count matrix.

[ATAC-Seq data analysis](https://training.galaxyproject.org/topics/epigenetics/tutorials/atac-seq/tutorial.html)
Visualizing output in pyGenomeTracks

By [Lucille Delisle](https://training.galaxyproject.org/training-material/hall-of-fame#lldelisle), [Maria Doyle](https://training.galaxyproject.org/training-material/hall-of-fame#mblue9), [Florian Heyl](https://training.galaxyproject.org/training-material/hall-of-fame#heylf)

Learn ATAC-Seq analysis with data from the study of Buenrostro et al. 2013, the first paper on the ATAC-Seq method. Compare predicted open chromatin regions to known binding sites.

Other News

HacktoberFest 2019

Galaxy is participating in HacktoberFest, the annual drive for global contribution in the growth of open source software has begun. Sign up and make a pull request for documentation, new tools, or contribute to any of the Galaxy GitHub repositories to earn free GitHub and digitalocean swag.

HacktoberFest Logo
GenomeSpace shuts down November 15

The GenomeSpace project ends on November 15, 2019 due to expiration of its NHGRI funding and we will be shutting down the GenomeSpace servers on that date. Galaxy was a GenomeSpace-enabled tool from the beginning of GenomeSpace and worked closely to maintain that connection over the years.

Galaxy integration in InterMine 4.1.0

The latest release of InterMine adds configuration free data import/export with Galaxy. An InterMine tutorial in the Galaxy Training Network is coming...

See the full release announcement and release notes for more on this release.