November 2020 Galactic News

JXTX Foundation, Events, Platforms, Jobs, Pubs, ...

November 3rd 2020

In the November 2020 issue

Galaxy News

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


JXTX: The James P. Taylor Foundation for Open Science

James Taylor
Same mission, new name

The foundation continuing James's legacy of supporting Open Science has been renamed from JTech to JXTX: The James P. Taylor Foundation for Open Science. The JXTX Foundation will continue to focus on mentoring and enabling junior researchers to participate in the Open Science James was dedicated to.

Meet the first class

The JXTX Foundation's first activity is to sponsor 10 graduate students to attend the 2020 Biological Data Science Conference at Cold Spring Harbor Laboratory. Awards were competitive and we are delighted to support this first cohort of awardees.

Big shoes to fill
Help move Open Science forward

You can help continue James's legacy of open and reproducible science by contributing to JXTX: The James P. Taylor Foundation for Open Science.


Event News

Despite COVID-19, there is still a lot going on. Some of it is virtual, but live events are starting to happen again, especially in Europe. We have updated our list of events to reflect what we know. Some highlights:

Galaxy Developer Roundtable

There will be one roundtable meetup this month, on November 12. Discussion will focus on working with the Galaxy Training Network.

Paper Cuts November

Paper Cuts are annoying but easy to fix bugs. The first Paper Cuts event in October was a smashing success, so we are going to do it again on November 18. Our second one-day Paper Cuts contribution fest will also be a 24-hour event spanning all time zones with our worldwide community.

Please save the date! It's an ideal opportunity for newcomers to become a Galaxy contributor.

du novo Webinar

This November 10 webinar by Barbara Arbeithuber​ and ​Nick Stoler will present Du Novo Sequencing, a method that can achieve <1% variant detection,​ by removing the reliance on a reference sequence, preserving a higher proportion of the input reads, and being available for Galaxy.

Galaxy Australia
Whats Up Down Under?

Three Galaxy Australia events are being offered by in November:

Galaxy Training Network day - (online) CoFest and community call

19th of November, Online

A dedicated day of collaborative work on the training content and calls with the Galaxy training community. 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.

VIB Training

3rd of December, Online

This hands-on workshop will familiarize you with the Galaxy user interface & execute (label-free) proteomics data-analysis. Taught by Melanie Föll and Matthias Fahrner from the University of Freiburg.

Sponsors

7 au 10 décembre 2020, en visio

Un Hackathon pour partager des compétences en terme du développement logiciel et d'administration système des Interactive Tools de Galaxy. Limité à 25 participants.

Admin Training

Galaxy Admin Training is coming in January. It will be online and global, and registration will open this month. Watch Twitter, this web site, and Galaxy Gitter channels for the announcement.

Upcoming Events
Upcoming Events

There are more than 16 events before the end of the year:

  • workshops, CoFests, talks, ...
  • all of them are online.

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. Here's the recent platform news we know about:

GalaxyTrakr

The GalaxyTrakr server is provided by the US Food and Drug Administration to support food-borne pathogen research worldwide. A User Guide, FAQ, Videos, and Email support are available. An account is required and anyone working in public health can apply.

Galaxy Africa

Devoted to assisting researchers on the African continent, accelerate their genomics research and analyses. This public server is configured by the Galaxy Africa team, and hosted by the UseGalaxy.eu team.

Galaxy Australia

Galaxy Australia is now officially supporting 10,000 researchers to analyse their valuable data. It's rapidly becoming the essential research tool for so many around the world.

Galaxy Europe

Galaxy EU has surpassed 20,000 users!

5 continents, 100 countries, more than 100 industry companies, 4,000 users trained using TIaaS, 11 million jobs, 12 jobs per minute...

UseGalaxy.*

Galactic Blog Activity

By Leighton Pritchard.

Leighton reports on the University of Strathclyde's experience teach Advanced Microbiology using UseGalaxy.eu's Training Infrastructure as a Service (TIaaS).

Spoiler: It went well.

SARS in JBrowse

Doc, Hub, and Training Updates

Metaproteomics analysis with metaQuantome

By Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Emma Leith, Marie Crane, and Praveen Kumar

A three part series on doing metaproteomics analysis with metaQuantome:

  1. Data Creation
  2. Function
  3. Taxonomy

metaQuantome

This tutorial got a thorough update from Mallory Freeberg.

VCFfilter

By Helena Rasche

Based on the work by Delphine Larivière and James Taylor with their COVID-19 Lectures, we have implemented a similar feature in the Galaxy Training Network. Learn how to use it.

Video

Publications

Pub curation activities are on hiatus right now but a few publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library anyway. Here are the new open access Galactic and Stellar pubs:

Rivière, E., Heupink, T. H., Ismail, N., Dippenaar, A., Clarke, C., Abebe, G., Heusden, P., Warren, R., Meehan, C. J., & Van Rie, A. (2020). Briefings in Bioinformatics. doi: doi.org/10.1093/bib/bbaa246

VijayKrishna, N., Joshi, J., Coraor, N., Hillman-Jackson, J., Bouvier, D., Beek, M. van den, Eguinoa, I., Coppens, F., Golitsynskiy, S., Stolarczyk, M., Sheffield, N. C., Gladman, S., Cuccuru, G., Grüning, B., Soranzo, N., Rasche, H., Langhorst, B. W., Bernt, M., Fornika, D., … Blankenberg, D. (2020). BioRxiv, 2020.10.09.327114. doi: 10.1101/2020.10.09.327114

Tekman, M., Batut, B., Ostrovsky, A., Antoniewski, C., Clements, D., Ramirez, F., Etherington, G. J., Hotz, H.-R., Scholtalbers, J., Manning, J. R., Bellenger, L., Doyle, M. A. , Heydarian, M., Huang, N., Soranzo, N., Moreno, P., Mautner, S., Papatheodorou, I., Nekrutenko, A., Taylor, J., Blankenberg, D., Backofen, R., Grüning, B. (2020). GigaScience, 9(10). doi: 10.1093/gigascience/giaa102

Timme, R., Laxmi, S., Balkey, M., Randolf, R., Wolfgang, W., & Strain, E. (2020). Protocols.io. doi: 10.17504/protocols.io.bdvfi63n

de Koning, W., Miladi, M., Hiltemann, S., Heikema, A., Hays, J. P., Flemming, S., van den Beek, M., Mustafa, D. A., Backofen, R., Grüning, B., & Stubbs, A. P. (2020). GigaScience, 9(10). doi: 10.1093/gigascience/giaa105

Goonasekera, N., Mahmoud, A., Chilton, J., Afgan, E. (2020). Bioinformatics. doi: 10.1093/bioinformatics/btaa860

Who's Hiring

Università degli Studi di Bari Aldo Moro, Regione Puglia, Italy.

Development and implementation of a computing platform in a cloud environment with a web interface based on the Galaxy workflow management system to provide access to computational tools for Precision Medicine compliant with GDPR directives.

Applications close 14 November.

Università degli Studi di Bari Aldo Moro

Roche, Bay Area, California, United States.

  • Lead data mining for biomarker discovery for medical conditions of interest.
  • Develop Agile Assay Design (AAD) tools for qPCR tests.
  • NGS data analysis tools and/or workflows.
  • Use these tools & workflows for R&D projects.
  • Deploy these tools on Roche intranet (Galaxy) and train scientists to use them.

Roche

ELIXIR Norway Team, University of Oslo, Norway.

Join the ELIXIR development / operations team at the University of Oslo (UiO), participating in the development, implementation and operation of functionality for various national and international solutions provided by ELIXIR Norway, including UseGalaxy.no and NeLS.

University of Oslo

Johns Hopkins University, Baltimore, Maryland, United States.

Provide technical expertise and oversight for the AnVIL Project, which incorporates Galaxy, Bioconductor, Terra, Gen3, and Dockstore into a secure cloud-based software ecosystem for genomic data analysis.

AnVIL

Help with Galaxy-P tools and workflow development, and general support for Galaxy implementation at the Minnesota Supercomputing Institute.

University of Minnesota

The Blankenberg Lab in the Genomic Medicine Institute at the Cleveland Clinic Lerner Research Institute is searching for Software Engineers and Postdoctoral Fellows. We utilize high-throughput omics technologies, such as Next-Generation Sequencing, and data-intensive computing to explore biomedical research questions.

Cleveland Clinic

A 3-year position of genomic data analyst is available to work within the "COllaborative NEtwork on research for Children and Teenagers with Acute Myeloblastic Leukemia" CONECT-AML framework.

The project is funded by the Institut National de Recherche sur le Cancer (INCA) and the Fight Kids Cancer programme. It involves 10 participant teams across France, with clinical or fundamental approaches.

ARTbio

The Schatz Lab at Johns Hopkins University is looking for:

  • Self-driven individuals that can work independently to fill multiple software development positions on the Galaxy Project.
  • Ambitious individuals to fill a programmer analyst position working on the Galaxy and AnVIL projects.

Johns Hopkins

Releases

Galaxy Language Server implements the Language Server Protocol to assist in the development of Galaxy tool wrappers inside modern code editors.

Please note this is still an early work in progress and bugs and issues are expected.

It provides realtime XML validation, code completion, help/documentation and other smart features to help in following best practices during the development process of XML tool wrappers for Galaxy.

The Galaxy Tools Visual Studio Code extension that uses the Galaxy Language Server can be downloaded from the Open VSX Registry and the Visual Studio Marketplace.

Galaxy Language Server

Other news

A group of Freiburg researchers provide global, open access to data on the SARS-CoV-2 genome which could hold the key for a new approach to treating the virus.

Uni Freiburg