December 2018 Galactic News
Platforms Directory; new events, pubs, blog posts, servers, tools and releases
The December 2018 Galactic News is here! This is a summary of what is going on in the Galaxy community. Here's what's happening:
- Galaxy Help: A new Q\&A site for Galaxy
- 170 new publications, including eight highlighted ones
- Galaxy Platform News: Three new public servers/services, and eight containers added to the platform directory.
- Two new Galactic Blog entries
- 16 Open positions in 7 countries on 3 continents.
- Doc, Hub, and Training Updates
- ToolShed contributions
- Planemo 0.57.1
- And other news too
If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.
Galaxy Help: A new Q\&A site for Galaxy
We are pleased to announce Galaxy Help, the new Galaxy Community Q\&A web site. Galaxy Help joins the Galaxy Gitter channels, Galaxy mailing lists and the Galaxy Hub as another place to get answers to your Galaxy related questions.
Galaxy Help replaces Galaxy BioStars, which is being retired after almost 5 years of service. (Galaxy BioStars was itself a replacement for the earlier galaxy-user mailing list.) The Galaxy BioStars site will remain up as a read-only archive (and will still be searched by the Galaxy Hub search).
Event News
Tired of sitting in the same old office/lab/cafe? Here are some upcoming events to help get you out and about.
2019 Galaxy Admin Training: Advance Registration Closes Dec 31
Advanced registration ends December 31. Register now and avoid the 45 to 60% price increase in the new year.
Galaxy Admin Training will be offered January 28 through February 1 at Penn State University, where the Galaxy Project got started over ten years ago. The workshop is split into a 2 day introductory session and a 3 day advanced topics session. Participants can register for one or both sessions. See the Galaxy 2019 Admin Training page for more details.
Nominate Topics for GCC2019 Training!
The 2019 Galaxy Community Conference (GCC2019) will be held in be held in Freiburg, Germany, 1-6 July. Like previous Galaxy Community Conferences, GCC2019 will feature invited keynotes, accepted talks, posters, demos, birds-of-a-feather gatherings and training. The format of GCC2019 will be a bit different than the previous years: it starts with 1 day of training and then 3 days with more specialized training sessions aligned with talks. You can read more about the new format on the conference FAQ.
The training topics that are offered are determined by the community so BY YOU!
Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations.
Nominated topics can cover a wide range. For example:
- Introduction to Using Galaxy
- Scientific topic oriented trainings
- Community specific trainings
- Development and administration around Galaxy
- Train the trainers
This list only shows some examples. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see the topic nominated in: 2016, 2015, 2014, 2013 and the Galaxy Events page.
Training nomination is open from December, 1st to December, 31. Topics will be compiled into a uniform list by the GCC2019 Organizing Committee, and topics will be voted on by the Galaxy Community from January, 15th to January, 31st.
GCCBOSC 2018 Videos are now available
We are pleased to announce that videos from GCCBOSC 2018 are available online and are linked to from the conference web site. Talks from the GCC parts of the meeting are available on a Galaxy Vimeo channel, and talks from the BOSC parts are available on a BOSC YouTube channel (and joint keynotes are available on both). There are over 70 presentations across both channels, showing every talk from the opening keynote to the closing keynote.
If you want to know more about what happened at GCCBOSC 2018, take a look at these meeting reports:
- GCCBOSC 2018 post-meeting report, by Nomi Harris
- City of roses they call it – Portland Oregon (USA), by Farah Zaib Khan
- The color of bioinformatics: what is it and how can it be modified?, by Tendai Mutangadura
- Code is Science at GCCBOSC, by Yo Yehudi
- Event photo album, by Bérénice Batut
- Final Conference Program (PDF)
See you next year in Freiburg (Galaxy) and Basel (BOSC)!
And, taking considerably less time than the GCCBOSC 2018 videos...
European Galaxy Days: Slides are online
Slides for presentations at European Galaxy Days are now online. EGD2018 featured almost 20 talks spanning the Galactic specturm, from implementation to application. Take a look.
Upcoming events
These and other Galaxy related events are coming up in the next few months:
| Date | Topic/Event | Venue/Location | Contact |
|---|---|---|---|
| December 3rd 2018 | Galaxy-P @ Metaproteome Symposium 2018 |  Helmholtz-UFZ, Leipzig Germany |
Pratik Jagtap, Tim Griffin, Magnus Arntzen, Praveen Kumar |
| December 6th 2018 | Molecular Dynamics and Analysis using BRIDGE |  Cape Town, South Africa |
Organizers |
| January 8th 2019 | Introduction to Galaxy |  Washington, DC |
 Dr. Ian Toma (itoma at gwu dot edu) |
| January 12th 2019 | Galaxy @ Plant & Animal Genome XXVII (PAG 2019) | San Diego, California |
Presenters |
| January 23rd 2019 | Cloud Resource Federation for Galaxy |  Online |
Enis Afgan |
| January 28th 2019 | **2019 Galaxy Admin Training** | Penn State University, State College, Pennsylvania, United States |
Instructors |
| February 4th 2019 | Traitement de données de séquences par Galaxy | AGROCAMPUS OUEST, Rennes, France |
Sandrine Lagarrigue |
| February 25th 2019 | Galaxy HTS data analysis workshop | University of Freiburg, Freiburg, Germany |
contact at usegalaxy.eu |
| July 1st 2019 | **2019 Galaxy Community Conference (GCC2019)** | Freiburg, Germany |
Organizers |
Publications
170 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in November.
Highlighted Publications
Galactic and Stellar publications from November.
- Laniakea: an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures, Marco Antonio Tangaro, Giacinto Donvito, Marica Antonacci, Matteo Chiara, Pietro Mandreoli, Graziano Pesole, Federico Zambelli. bioRxiv doi: 10.1101/472464
- Aequatus: an open-source homology browser, Anil S Thanki, Nicola Soranzo, Javier Herrero, Wilfried Haerty, Robert P Davey. GigaScience, Volume 7, Issue 11, 1 November 2018, giy128, doi: 10.1093/gigascience/giy128
- Automatic generation of bioinformatics tools for predicting protein–ligand binding sites, Yusuke Komiyama, Masaki Banno, Kokoro Ueki, Gul Saad, Kentaro Shimizu. Bioinformatics, Volume 32, Issue 6, 15 March 2016, Pages 901–907, doi:10.1093/bioinformatics/btv593
- Workflow-based automatic processing for Internet of Floating Things crowdsourced data, Raffaele Montella, Diana Di Luccioa, Livia Marcellino, Ardelio Galletti, Sokol Kosta, Giulio Giunta, Ian Foster. Future Generation Computer Systems, Volume 94, May 2019, Pages 103-119 doi: 10.1016/j.future.2018.11.025
- FAIRness and Usability for Open-Access Omics Data Systems, Daniel C. Berrios, Afshin Beheshti, Sylvain V. Costes. AMIA 2018 Annual Symposium
- SyNDI: synchronous network data integration framework, Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos and Maria Suarez-Diez. BMC Bioinformatics 201819:403 doi: 10.1186/s12859-018-2426-5
- Satellite DNAs Unveil Clues about the Ancestry and Composition of B Chromosomes in Three Grasshopper Species, Diogo Milani, Vanessa B. Bardella, Ana B. S. M. Ferretti, Octavio M. Palacios-Gimenez, Adriana de S. Melo, Rita C. Moura, Vilma Loreto, Hojun Song and Diogo C. Cabral-de-Mello. Genes 2018, 9(11), 523; doi: 10.3390/genes9110523
- FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative, Natalie J Stanford, Finn Bacall, Fatemeh Zamanzad Ghavidel, Martin Golebiewski, Inge Jonassen, Rune Kleppe, Olga Krebs, Hadas Leonov, Stuart Owen, Kjell Petersen, Maja Rey, Stian Soiland-Reyes, Kidane Tekle, Andreas Weidemann, Alan Williams, Ulrike Wittig, Katy Wolstencroft, Anders Goksøyr, Jacky L. Snoep, Jon Olav Vik, Wolfgang Müller and Carole Goble. NETTAB 2018
Seven out of eight of these papers are open access.
Publication Topics
| # | Tag | # | Tag | # | Tag | # | Tag | |||
|---|---|---|---|---|---|---|---|---|---|---|
| 109 | +Methods | 40 | +UsePublic | 23 | +UseMain | 22 | +Workbench | |||
| 17 | +RefPublic | 11 | +Reproducibility | 10 | +UseLocal | 6 | +Tools | |||
| 5 | +IsGalaxy | 3 | +Other | 3 | +Shared | 2 | +Cloud | |||
| 1 | +Visualization |
Galaxy Platforms News
The Galaxy Platform Directory was launched lat month. It lists every resources for easily running your analysis on Galaxy, including publicly available servers, cloud services, and containers and VM that run Galaxy.
BioBix
The BioBix server is a Galaxy genomics server with many of the "standard" Galaxy tools for genomics. It also includes PROTEOFORMER tools. PROTEOFORMER is a proteogenomic pipeline that delineates true in vivo proteoforms and generates a protein sequence search space for peptide to MS/MS matching. BioBix is hosted by the Lab of Computational Genomics & Bioinformatics at Ghent University, Belgium. See the server description for more details.
Laniakea / INDIGO-DataCloud
Laniakea provides Italy-based researchers the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians, with built-in storage encryption for user data. See the service description for full details.
Hardwood Genomics
The Hardwood Genomics Project has launched a simplified, workflow-centered interface to Galaxy. Workflows for quality control, short read mapping, functional gene annotation, RNA-Seq differential gene expression and variant analysis.
UseGalaxy.eu Hardware Upgraded
The head node for UseGalaxy.eu was upgraded on 12 November and there was no interruption of service.
New Containers
This month several containers were added to the directory. These aren't actually new containers, but they are new in the platform directory:
- Constructive Solid Geometry
- deepTools
- Exome-Seq
- Galaxy BLAST+
- Galaxy for basic sequence manipulation
- Galaxy for Imaging
- Galaxy Genome Annotation
- Workflow4Metabolomics
All of these are Docker containers.
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 | |||
|---|---|---|---|---|---|---|---|---|---|---|
| 15 | >Huttenhower | 5 | >RepeatExplorer | 3 | >Cistrome | 3 | >Galaxy-P | |||
| 3 | >UseGalaxy.eu | 3 | >Workflow4Metabolomics | 2 | >ARIES | 2 | >Nebula | |||
| 2 | >PIPE-CLIP | 2 | >RiboGalaxy | 2 | >UTProt | 1 | >ARGs-OAP | |||
| 1 | >BioBix | 1 | >CBIB | 1 | >ChemFlow | 1 | >CPT | |||
| 1 | >CTMM-TRAIT | 1 | >EpiToolKit | 1 | >FACE-IT | 1 | >GeneLab | |||
| 1 | >Laniakea | 1 | >NeLS | 1 | >NGS-QC | 1 | >Pasteur | |||
| 1 | >PhenoMeNal | 1 | >Pitagora | 1 | >PreSTIGE | 1 | >SouthGreen | |||
| 1 | >SymD | 1 | >UseGalaxy.org |
New Galactic Blog Posts
There are two new Galactic Blog entries:
- Galaxy Tool Generator (GTG), by Ming Chen
- Tutorial of the Month: "Reference-based RNA-Seq data analysis", selected by Saskia Hiltemann, by Bérénice Batut
Who's Hiring
The dark energy* of irreproducible research is threatening the science universe! Please help the Galaxy expand!
- Chief Scientific Officer University of Cape Town, South Africa. Develop a comprehensive database, informatics tools and toolsets on a Galaxy/web bioinformatics server.
- M2 - bio-informatique, Laboratoire de Virologie , Hôpital St Louis, Paris, France.
- Cloud Computing Bioinformatics Programmer working with IRIDA, Simon Fraser University, Vancouver, Canada
- M2 - Epigénétique : effet de la température sur le méthylome lors de la masculinisation du tilapia du Nil, UMR 116 ISEM au Cirad, Campus International de Baillarguet, Montpellier, France
- Platform technical support, University of Barcelona, Spain. Experience in working and developing tools for Galaxy
- Réalisation d’outils Galaxy pour l’analyse de données GCMS au sein de la Plateforme d’Exploration du Métabolisme, INRA de Clermont Ferrand-Theix, France
- Senior IT DevOps Data Engineer, Adaptimmune, Abingdon, Oxfordshire, United Kingdom. Required: Experience with following bioinformatic pipeline tools: Galaxy…
- Principal Technical Business Development Manager: AWS Research in Biomedical, Amazon Web Services, United States
- 2-year IR/postdoc position (Analysis of Genomic Variants in Children and Young Adults with Acute Myeloid Leukemia), Analyse Bioinformatique ARTbio, Paris, France
- Bioinformatics Scientist, ResearchDx, Irvine, California, United States
- NGS Scientific Applications Specialist, Integrated DNA technologies, Iowa City, Iowa, United States
- Scientist (f/m), NGS bioinformatics core facility, Helmholtz Zentrum München, Germany
- Galaxy Developers, Intero Life Sciences, United States.
- Freiburg Galaxy Team has open positions, Freiburg, Germany
- The Blankenberg Lab in the Genomic Medicine Institute at the Cleveland Clinic Lerner Research Institute is hiring postdocs.
- Galaxy Project is hiring two software engineers at Johns Hopkins University: distributed computing engineer and a full stack developer; see [this for more details on the positions](https://jobs.jhu.edu/job/Baltimore-Software-Engineer-MD-21218/442289500/, Baltimore, Maryland, United States).
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
There was a mind-boggling amount of activity in the Galaxy Training Materials in November, and some Hub activity as well:
Training Materials
- New Basics of Machine Learning Tutorial by Anna Syme, Anup Kumar, and Levi Baber.
-
New Proteogenomics tutorials by Subina Mehta
- New Mass spectrometry imaging 1: Loading and exploring MSI data, by Melanie Foell
- New Introduction to Metabolomics slides by Gildas Le Corguillé and Cécile Canlet
-
New Tutorials on how to Teach and Host Galaxy Training by Bérénice Batut, Helena Rasche, and Saskia Hiltemann:
- Update to Visualization of RNA-Seq results with CummeRbund by Andrea Bagnacani
And a few enhancements to the training materials website
- Automatic translation of tutorials into 5 languages (français, 日本語, Español, Português, and العربية), by Bérénice Batut.
- A new Learning Paths feature was implemented by Bérénice Batut to show a list of recommended follow-up tutorials at the end of the hands-on training manuals.
- Training Philosophies added by Helena Rasche. We all teach Galaxy in different ways depending on our audience, surroundings, culture and preferences. Instructors can now share their own training stories and read about those of others. Add your own here!
- More flexible training material hosting and incremental build support by Mehmet Tekman
- Site search searches the entire TeSS catalog of training materials (which includes all of the Galaxy Training materials).
And we would especially like to welcome new contributors Anup Kumar, Andrea Bagnacani, Subina Mehta, Cécile Canlet.
Hub
ToolShed Contributions
](http://toolshed.g2.bx.psu.edu/)Tool Shed contributions in November 2018.
Releases
New additions to the Galaxy Ecosystem.
Planemo 0.57.1
Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included numerous fixes and enhancements.
See GitHub for details.
Other News
-
From Andrew Page at the 4th Annual European Microbiome Congress, via Elizabeth Bik
- At the Quadram we will have 4 Illumina seqeuncers, 1 PromethION long read sequencer, and piles of minION sequencers. My team has 6 PhD level bioinformaticians and computer scientists, and we use Galaxy.
-
From ELIXIR Europe
- ~ 4000 containers registered in BioContainers to enable sharing, exchange and reuse of bioinformatics software and facilitate reproducibility of life science research:
-
From Graham Etherington and Nicola Soranzo
-
From Björn Grüning
- If you want to test your Galaxy workflows against the European Galaxy server please contribute to UseGalaxy.eu Workflow Testing or contact us.