Summer (August) 2018 Galaxy News

Galaxy News

Welcome to the Summer 2018 Galactic News, 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.


GCCBOSC 2018 is done!

GCCBOSC 2018

GCCBOSC 2018 was held 25-30 June in Portland, Oregon, United States. The combination of the Galaxy Community Conference and the Bioinformatics Open Source Conference brought together 300 people over an 8 day period. GCCBOSC featured

  • 21 training sessions covering 16 topics over 2 days,
  • 2+ days of conference sessions with 3 keynotes, 29 accepted talks, 37 lightning talks, and 1 panel,
  • Two Poster and Demo sessions, with 88 poster and demo presentations,
  • 19 Birds-of-a-feather gatherings, and
  • 4 days of collaborative work

Most posters and slides are now linked to from the conference web site. Videos of conference talks will be available within a month.

Conference Reports

2019 Galaxy Community Conference: 1-6 July, Freiburg, Germany

GCC2019

GCC2019 will be held in Freiburg, Germany, 1-6 July. Like previous Galaxy Community Conferences, GCC2019 will feature invited keynotes, accepted talks, posters, and demos, birds-of-a-feather gatherings, multiple days of collaborative work, and plenty of opportunities to network with your fellow data-intensive researchers and practitioners. If you are working in data-intensive life science, there is no better place to be.

Freiburg Germany

Freiburg is on the edge of the Black Forest, and is famous for its architecture, cobblestone streets and historic districts, and is home to one of Germany's oldest universities (and our host)!. Freiburg is in the Baden wine-growing region and is the sunniest city in Germany.

GCC2019 will be held at Konzerthaus Freiburg in central Freiburg, adjacent to the Freiburg train station.

GCC2019 is hosted by the Freiburg Galaxy Project, the University of Freiburg, and de.NBI (the German Network for Bioinformatics Infrastructure).

Galaxy Freiburg Project    University of Freiburg      de.NBI :the German Network for Bioinformatics Infrastructure


What about BOSC?

2018 was the first time GCC and BOSC held a joint conference. There is significant overlap between the communities and we had been considering a joint event since at least 2015. Organizers from both communities felt that GCCBOSC 2018 was a success, and that future joint meetings have even more potential for success. Not everything went as smoothly as it could have, but we now have a year's experience and a plethora of excellent feedback and suggestions from conference participants. Both the GCC and BOSC organizers feel that we should explore doing this again.

On the flip side, there are also significant reasons to not permanently join the conferences together: A permanently joint conference risks diluting both communities. GCC also has a different focus from ISMB (BOSC's usual conference partner), and many BOSCers (while still enthused about the GCC partnership) really hesitate to give that up. Planning a joint conference is also more work than planning a standalone GCC.

The Decision

Both sets of organizers, independently and simultaneously (that has to be a good sign :-), decided

  1. Not to hold a joint GCC and BOSC conference in 2019.
  2. To look into holding a joint meeting every few years, starting as soon as 2020.

This approach preserves both communities, and has the potential to further increase the synergy between the communities (which was our primary motivating goal in 2018). This also gets BOSC back to ISMB on a regular basis, and helps us avoid some logistical challenges a joint conference would pose in 2019.

A joint meeting in 2020 or 2021 depends on finding a suitable venue (300+ attendees, and more parallel events is just harder) and several other stars aligning, but our aim to bring these communities back together.

GTN CoFest on Metagenomics Training Material, 17 August

GTN cofest logo

The Galaxy Training Network is organizing regular online CoFests (Collaboration/Contribution Fests) every 3 months on the 3rd Friday for a day of the collaborative work on the training content.

The first one will be on the 17th of August. We plan to focus on metagenomics training; but anyone who would like to contribute on any other topics is very welcome to join. We will coordinate via the GTN Gitter channel and GitHub issues.

2018 SACNAS Workshops


Preconference data workshops at 2017 SACNAS Meeting

Software Carpentry

Data Carpentry

CyVerse

Galaxy

If you are attending the 2018 SACNAS meeting in San Antonio in October, then please consider signing up for one of these preconference workshops:

Software and Data Carpentry

Data Platforms for Life Science Researchers

Registration is free but space is limited. You are strongly encouraged to register soon. Both workshops are held October 10, the day before SACNAS starts.

Register Now

Plese note: The Galaxy Community Fund is augmenting SACNAS Travel Scholarships awards for the first ~ 28 scholarship recipients that register for these workshops. The additional funds will cover an extra night's lodging for scholarship recipients, enabling you to arrive the day before the workshops. Funds are limited, and once the funds are allocated, they are gone. (You must have received a SACNAS Travel Scholarship to be eligible.)

European Galaxy Days, 19-20 November, Freiburg, Germany

European Galaxy Days

European Galaxy Days will be held 19 and 20 November 2018 in Freiburg, Germany. The first day will give an overview of the current state of the Galaxy framework with several talks and demonstrations. The second day will focus on developing and extending the Galaxy ecosystem.

The event is free. Registration will open soon. See the event home page for more.

Gateways 2018

Gateways 2018

Gateways 2018 (September 25–27, at the University of Texas at Austin) early bird registration ends Monday! So, get on it.

Gateways are user-friendly interfaces (including Galaxy) to scientific computing, data, and other domain-specific resources to support research and education. The third Gateways annual conference is an opportunity for gateway creators and enthusiasts to learn, share, connect, and shape the future of gateways as part of a vibrant community with common interests.

Upcoming events

These and other Galaxy related events are coming up in the next few months:

DateTopic/EventVenue/LocationContact
August 7th 2018RNA-Seq analysis using GalaxyQFAB, St Lucia, Queensland, AustraliaTraining offered by GTN Membertraining@qfab.org
August 13th 2018Science Gateways BootcampChicago, Illinois, United Stateshelp@sciencegateways.org
August 17th 2018GTN CoFest on Metagenomics Training MaterialOnlineBérénice Batut, Saskia Hiltemann
August 22nd 2018Genome Assembly using Galaxy Australia University of Melbourne, James Cook University (Townsville + Cairns), University of Queensland, University of Southern Queensland, AustraliaTraining offered by GTN MemberAnna Syme
September 4th 2018Genome assembly using GalaxyQFAB, St Lucia, Queensland, AustraliaTraining offered by GTN Membertraining@qfab.org
September 12th 2018Variant Detection using Galaxy AustraliaUniversity of Melbourne, Victoria, AustraliaTraining offered by GTN MemberIgor Makunin
September 17th 20186th Galaxy high-throughput sequencing (HTS) data analysis workshopUniversity of Freiburg, Freiburg GermanyTraining offered by GTN MemberFreiburg Galaxy Team
September 18th 2018RNA-Seq analysis using GalaxyQFAB, St Lucia, Queensland, AustraliaTraining offered by GTN Membertraining@qfab.org
September 18th 2018Variant detection using GalaxyQFAB, St Lucia, Queensland, AustraliaTraining offered by GTN Membertraining@qfab.org
September 25th 2018Gateways 2018University of Texas, Austin, Texas, United StatesKatherine Lawrence
October 2nd 2018Genome assembly using GalaxyQFAB, St Lucia, Queensland, AustraliaTraining offered by GTN Membertraining@qfab.org
October 8th 2018Workflow4Experimenters 2018 CoursePasteur Institute, Paris, FranceTraining offered by GTN MemberGildas Le Corguillé
October 10th 2018SACNAS 2018 Pre-Conference Workshops2018 SACNAS, San Antonio, Texas, United StatesTraining offered by GTN MemberCamille Avestruz, Tracy Teal, Blake Joyce, Dave Clements, Joslynn Lee
October 15th 2018Analyse RNAseq sous GalaxyStation marine de Roscoff, FranceTraining offered by GTN Memberchristine.mantecon @upmc.fr
October 16th 2018Bioinformatique - Analyse avancée de séquencesBordeaux, FranceIntervenants
October 17th 2018Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach itVU, Amsterdam, The NetherlandsTraining offered by GTN MemberCelia van Gelder
November 12th 2018BioHackathon 2018 ParisCampus des Berges de Seine, Paris, FranceBérénice Batut, Hervé Ménager
November 14th 2018Analyse des données RNA-Seq sous l'environnement GalaxyLyon, FranceTraining offered by GTN Membercontact@biosciencesco.fr
November 19th 2018European Galaxy DaysFreiburg, GermanyHans-Rudolf Hotz, Björn Grüning, Jean-François Dufayard
July 1st 20192019 Galaxy Community Conference (GCC2019)Freiburg, GermanyTraining offered by GTN MemberOrganizers

Christophe Caron, 1968-2018

Christophe Caron

Christophe Caron passed away in May at the age of 50. Christophe was an extraordinary Galaxy community organizer and he is dearly missed. See the SFBI tribute page to Christophe and this Galaxy News item for more about Christophe, his passing, and his many contributions over the years.

Publications

417 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in May, June, and July.

Highlighted Publications

20 Galactic and Stellar publications.

This included a new paper to reference whenever using, extending, or referencing Galaxy:

A new paper to reference when discussing Galaxy in the context of reproducibility:

And a new paper to reference when discussing Galaxy training:

And a new paper to cite when discussing Galaxy in a cloud context:

Other highlighted papers include:

Publication Topics

# Tag # Tag # Tag # Tag
266 +Methods 98 +UsePublic 59 +Workbench 40 +UseMain
35 +RefPublic 27 +UseLocal 22 +Reproducibility 14 +Tools
14 +IsGalaxy 11 +Cloud 10 +Unknown 5 +Project
5 +Other 3 +HowTo 2 +Shared 2 +Visualization
1 +UseCloud

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

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.

New Galactic Blog Entries

Galactic Blog

There are two new Galactic Blog entry:

Public Galaxy Server News

There are over 100 publicly accessible Galaxy servers and six semi-public Galaxy services. Another public server was added in the past quarter:

ProteoRE

ProteoRE

"ProteoRE (Proteomics Research Environment) aims at centrally providing the proteomics community with an online research service enabling biologists/clinicians without programming expertise to annotate and interpret their proteomics data through the Web."

ProteoRE currently comprises tools (including graphical display) for:

  • Customary data manipulation (e.g. filtering, lists comparison, ID conversion…)
  • Protein list annotation (e.g. information retrieval from public resources - human species)
  • Functional analysis (e.g. GOterms frequencies, enrichment analysis) including graphical representation.
  • Pathway analysis (e.g. Reactome)

This version also includes Galaxy generic tools and some tools from the GalaxyP project that should be of great help for people who want to (re)process their MS-based proteomics data (e.g. peptide/protein identification). ProteoRE tools are in the Galaxy Toolshed.

See the ProteoRE pubic server directory page for more.

Public Servers in Publications

We tag papers that use, mention, implement or extend public Galaxy Servers. Here are the counts for the past 3 month's publications:

# Tag # Tag # Tag # Tag
38 >Huttenhower 18 >RepeatExplorer 13 >Workflow4Metabolomics 7 >ARGs-OAP
7 >Cistrome 6 >RiboGalaxy 5 >DeepTools 4 >UseGalaxy.eu
3 >ARGalaxy 3 >Galaxy-P 3 >Genomic Hyperbrowser 3 >Langille
3 >LAPPS Grid 3 >PIA 2 >ARIES 2 >CLIMB
2 >GVL-Cloud 2 >GVL-QLD 2 >NCGAS 2 >Orione
2 >UseGalaxy.org 1 >BioMaS 1 >BIPAA 1 >CoSSci
1 >CPT 1 >DeepVirome 1 >Dintor 1 >EpiToolKit
1 >GenAP 1 >GIO 1 >Globus Genomics 1 >IGGalaxy
1 >KREAP 1 >Martin Luther 1 >MetaNET 1 >Mississippi
1 >NeLS 1 >NGS-QC 1 >Osiris 1 >Palfinder
1 >Pasteur 1 >PhenoMeNal 1 >PL-Grid 1 >PreSTIGE
1 >RNA Workbench 1 >UseGalaxy.org.au

Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in May, June, and July 2018.

Hub and Doc Updates

Releases

18.05 Galaxy Release

GalaxyProject

The 18.05 release of Galaxy is out. Thanks to the Galaxy Committers and you, our community!

Highlights:

  • New Interface Style Library - Bootstrap 4 leading to VueJS
  • Unlimited Browser Upload Size - Chunked and resumable file uploads out-of-the-box
  • New Powerful Rule-Based Data Uploader - Use lists of rules for processing metadata tht describes the upload of arbitrarily complex collections
  • GDPR Beta Mode - We introduce beta GDPR privacy mode
  • New HIV-TRACE Plugin - Integration of a new visualization plugin - HIV-TRACE
  • Visualization Frameworks Unified - The charts and generic visualization frameworks have been merged together

See the full release notes for more.

Thanks for using Galaxy!

Galaxy Docker Image 18.05

The Galaxy Docker project has a matching release, for Galaxy 18.05. The release features the 18.05 enhancements.

Planemo 0.49.0-0.54.0

Planemo

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included numerous fixes and enhancements (~50 of them).

See GitHub for details.

galaxy-lib 18.5.8 - 18.5.13

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.

ephemeris 0.8-0.9

Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows. It has extensive documentation. These latest releases features numerous newly contributed features.

sequence_utils 1.1.3

Galaxy's sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats.

Earlier Releases

Other packages released since April.

Starforge 0.3.6

Starforge

Starforge is a collection of scripts that supports the building of components for Galaxy. Specifically, with Starforge you can:

These things will be built in Docker. Additionally, wheels can be built in QEMU/KVM virtualized systems. Documentation can be found at starforge.readthedocs.org.

The release features Python 3-compatible setup.py wrapping and a fix for pip 10.

BioBlend 0.11.0

BioBlend is a Python library for interacting with CloudMan and Galaxy‘s API. BioBlend makes it possible to script and automate the process of cloud infrastructure provisioning and scaling via CloudMan, and running of analyses via Galaxy.

See the release notes for what's new in release 0.11.0.

And the rest ...

Other Galaxy packages that haven't had a release in the past four months can be found on GitHub.

Other News