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March 2019 Galactic News
GalaxyAdmins, GCC2019 Childcare sponsors, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more!
2019-03-04

Galaxy News

The March 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 Sponsors

We are very pleased to announce that eLife and F1000Research are first two sponsors for GCC2019. And they are both sponsoring childcare. Yes, there will be childcare at GCC2019!

eLife

eLife

eLife is a non-profit open access journal, publishing research from across the life and biomedical sciences. We also invest heavily in software development, new product design, collaboration and outreach. This includes the development of open-source tools, with extensible capabilities, that can be used, adopted and modified by any interested party to help move towards an ecosystem that serves science and scientists as efficiently and as cost-effectively as possible.

Have you got an idea that will bring cutting-edge technology to open research communication? We are here to help.

eLife’s Innovation Initiative was set up to identify and support innovative, small-to-medium-scale open-source projects aiming to improve the sharing and reuse of scientific discoveries. The primary outputs of the Initiative are open tools, technologies and processes aimed at improving the discovery, sharing, consumption and evaluation of important scientific research.

Through this Initiative, we’re always on the lookout for opportunities to engage with the best emerging talent and ideas at the interface of research and technology. You can find out more about some of these engagements on eLife Labs, or contact our Innovation Community Manager for more information (innovation@elifesciences.org).

The Galaxy Gateway on F1000Research

F1000Research: Open for Science

F1000Research is proud this year to be sponsoring childcare for GCC2019, which we feel is vital for inclusivity. F1000Research is an Open Access publishing platform for the life sciences that publishes a range of different article types, from traditional research articles, to method articles and software tools. The platform is particularly well suited to publishing software tool articles as our versioning system allows small updates at any time, we have proper syntax highlighting and we can support LaTeX and markdown submissions.

Our Galaxy Gateway on the platform brings together articles, posters and slides from Galaxy events. The Gateway allows authors to quickly share their work with the community, boosting visibility and giving researchers proper credit for their contribution.

We’re pleased to be running a call for papers for GCC2019 and would like to invite the Galaxy community to submit their articles to the Galaxy Gateway by 20th July 2019. These can be any type of article, such as a new Galaxy workflow or an update to an existing method or software tool. This is a great opportunity to shine a light on your research, improve its impact and be credited with an academic paper for your work. Please submit via the Galaxy gateway and if you have any questions at all do not hesitate to get in touch at publishers@f1000.com.

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).

GalaxyAdmins

[GalaxyAdmins](/src/community/galaxy-admins/index.md)

Kubernetes

After a two year hiatus, the online GalaxyAdmins meetups will return on March 21, with a community discussion, and a presentation from Pablo Moreno on Running Galaxy on Kubernetes, online at 15:00 GMT (see your local time). See the meetup page for links).

GalaxyAdmins is a discussion group for Galaxy community members who are responsible for Galaxy installations. Our online meetups are around an hour long and feature a presentation followed by an open discussion. It's a great place to catch up on what your fellow admins are thinking about.

Upcoming events

These and other Galaxy related events are coming up:

Date Topic/Event Venue/Location Contact
March 6th 2019 Galaxy for linking bisulfite sequencing with RNA sequencing University of Rostock, Rostock, Germany Training offered by GTN Memberdestair [at] leibniz-fli.de
March 18th 2019 Gatersleben Research Conference: Applied Bioinformatics for Crops Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany Björn Grüning
March 20th 2019 Introduction into Galaxy and how to design your own analysis workflow Computational Biology Starter, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany Anne Fiebig
March 21st 2019 GalaxyAdmins February 2019 Meetup Online Helena Rasche, Dave Clements
March 21st 2019 RNAseq analysis with Galaxy Sorbonne Université, Paris, France Training offered by GTN Memberhttps://gitter.im/ARTbio/Hotline
April 1st 2019 Getting started with Galaxy and NGS Platforms QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
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 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 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.
July 1st 2019 2019 Galaxy Community Conference (GCC2019) Freiburg, Germany Training offered by GTN MemberOrganizers

Publications

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

Highlighted Publications

Galactic and Stellar publications from February:

Five of the eight highlighted publications are open access.

Publication Topics

New Tag: Education

We added a new tag to the Galaxy Publication Library this month: Education. This tag highlights papers that focus on training, teaching, and/or education in general. Galaxy is well suited for teaching bioinformatics and this has been reflected in publications for several years. There are three new pubs this month about education. We also selectively back-curated several papers. Education is the first new tag added to the library in six years.

# Tag # Tag # Tag # Tag
124 +Methods 50 +UsePublic 27 +Workbench 26 +UseMain
16 +UseLocal 12 +RefPublic 8 +Tools 7 +IsGalaxy
7 +Reproducibility 4 +Cloud 3 +Education 2 +HowTo
2 +Shared 1 +Other

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 February:

FreeBioInfo

FreeBioInfo

FreeBioinfo is a public server for metagenomic analysis. The server supports a wide range of metagenomics and other tools. Ther is a Cookbook for the site (although it is in Chinese). FreeBioInfo is hosted at the China Agricultural University, in Beijing, China.

GCAC

GCAC

GCAC : Galaxy for Compound Activity Classification is available as a public server, as a virtual machine, and as a tool suite in the Galaxy Toolshed. GCAC is a web enabled paltform for predictive model building using R and caret package for virtual screening. GCAC is a one stop solution for data generation, data preparation, feature selection, model building, prediction and retrieval of potential lead molecules. The GCAC Manual describes how to use the service. GCAC is supported by Jawaharlal Nehru University.

EWAS-Galaxy

EWAS-Galaxy is a Docker image for population epigenetics data analysis. Epigenome-wide association studies (EWAS) analyse genome-wide activity of epigenetic marks in cohorts of different individuals to find associations between epigenetic variation and phenotype. EWAS-Galaxy is supported by the University of Bradford.

Mandoiu Lab

Mandoiu Lab

The Mandoiu Lab Galaxy server is a customized installation of the Galaxy framework deploying bioinformatic tools and pipelines developed in the Mandoiu Lab at the University of Connecticut for high-throughput sequencing and immunogenomics data analysis. Source code and relevant publications for these and other tools developed in the lab are available on the Mandoiu lab software page.

DocMethyl

DocMethyl EpiMOLAS is Docker image for DNA methylation analysis in WGBS. This Galaxy docker container have tested with demo dataset under the Ubuntu 16.04 64 bit system equipped with four-core CPU, 32GB RAM, 400GB storage. The image is maintained by the Institute of Information Science, Academia Sinica, in Taipei, Taiwan.

Trinity

Trinity CTAT

Trinity CTAT Galaxy is a public server and Docker container providing users with access to large memory resources required for de novo transcriptome assembly and downstream analysis. Funded by the National Cancer Institute, the Trinity Cancer Transcriptome Analysis Toolkit provides a suite of software for the analysis of cancer transcriptome data. The nature of cancer data requires different assumptions and approaches to analysis, above and beyond the normal challenges of dealing with RNA-seq. View more information on the tools available here. The resource has slides available for tasks such as moving data, and help can be reached at trinity@ncgas.org. There are no quotas, however, there is an aggressive purge policy for the disk usage. Files over 60 days old are removed by the system. An account is needed to access the resource and users are asked to fill out a registration form about your research (this helps us stay funded).

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
21 >Huttenhower 6 >RepeatExplorer 5 >APOSTL 5 >Workflow4Metabolomics
3 >Cistrome 2 >Galaxy-P 2 [>Globus Genomics](https://www.zotero.org/groups/1732893/galaxy/items/order/dateAdded/sort/desc/tag/>Globus Genomics) 1 >ABiMS
1 >CPT 1 >epiGeEC 1 >EWAS-Galaxy 1 >FreeBioinfo
1 >G-OnRamp 1 >GalaxEast 1 >GCAC 1 >GVL-Unspecified
1 >Langille 1 >Mandoiu 1 >MGEScan 1 >Nebula
1 >Palfinder 1 >Pasteur 1 >PhenoMeNal 1 >RiboGalaxy
1 >Sciensano 1 >SMAGEXP 1 >UseGalaxy.eu 1 >VirAmp
1 >ZBIT

Galactic Blog

New Galactic Blog Post

This month we have a Galactic Blog post where Nate Coraor was interviewed about what CVMFS actually is and what it does for Galaxy.


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 February, and the Hub as well:

GTN Training Materials

Galaxy Training Materials

There was a tremendous amount of content added to the GTN while our fearless instructors of the 2019 Galaxy Admin Training faced below freezing temperatures in the unforgiving mountains of Pennsylvania. A warm thanks to Helena Rasche, John Chilton, Marten Cech, Nate Coraor, and Simon Gladman for adding to the growing Galaxy Server Administration section of the GTN. See these training materials below:


ToolShed Contributions

Tool Shed contributions in February 2019 (there were a lot).

Releases

New additions to the Galaxy Ecosystem.

Galaxy Release 19.01

We are pleased to announce the release of Galaxy 19.01. This release includes the revised UI style, addition of colorful tags, extensive workflow enhancements, and enhanced support for Singularity.

Please see the release notes for additional information.

galaxy-lib 19.5.0

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

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