October 2018 Galactic News
New events, pubs, blog posts, servers, tools and releases (and a Galaxy song too)
- New Galactic Blog Posts
- Who's Hiring
- Other News
The October 2018 Galactic News is here! This is a summary of what is going on in the Galaxy community. Here's what's happening:
- 2018 SACNAS Workshops Still space, still free!
- European Galaxy Days, 19-20 November, Freiburg, Germany
- 2019 Galaxy Admin Training
- All upcoming events
- 200 publications, including 10 highlighted ones
- Three new Galactic Blog entries (one of them contains a Galaxy Song)
- Open positions with 5 organizations
- Public Galaxy Server News
- ToolShed contributions
- And other news too
If you have anything to add to next month's newsletter, then please send it to email@example.com.
Tired of sitting in the same old office/lab/cafe table? Here are some upcoming events to help get you out and about.
2018 SACNAS Pre-conference Workshops
If you will be anywhere near San Antonio, Texas on October 10 then please consider participating in one of these SACNAS preconference workshops. You don't need to be registered for the 2018 SACNAS meeting to attend. Everyone is eligible and the workshops are free.
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.
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 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 and registration is open. See the event home page for more.
2019 Galaxy Admin Training
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.
Registration is open. Early registration rates end October 31st.
See the Galaxy 2019 Admin Training page for more details.
These and other Galaxy related events are coming up in the next few months:
200 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in September.
10 Galactic and Stellar publications.
Federated Galaxy: Biomedical Computing at the Frontier by Enis Afgan, Vahid Jalili, Nuwan Goonasekera, James Taylor, Jeremy Goecks. 2018 IEEE 11th International Conference on Cloud Computing (CLOUD) (PDF).
Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery by Nagamani, S., Gaur, A. S., Tanneeru, K.,Muneeswaran, G.,Madugula, S. S., MPDS Consortium, Druzhilovskiy, D., Poroikov, V. V., and Sastry, G. N. SAR and QSAR in Environmental Research.
OpenMinTeD: A Platform Facilitating Text Mining of Scholarly Content by Labropoulou, P., Galanis, D., Lempesis, A., Greenwood, M.A., Knoth, P., de Castilho, R.E., Sachtouris, S., Georgantopoulos, B., Anastasiou, L., Martziou, S., Gkirtzou, K., Manola, N., and Piperidis, S. WOSP 2018 Workshop Proceedings.
Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes by Peters, K., Gorzolka, K., Bruelheide, H., and Neumann, S. Scientific Data.
Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics by Sajulga, R., Mehta, S., Kumar, P., Johnson, J. E., Guerrero, C. R., Ryan, M. C., Karchin, R., Jagtap, P. D., and Griffin, T. J. Journal of Proteome Research.
Approaches for containerized scientific workflows in cloud environments with applications in life science by Spjuth, O., Capuccini, M., Carone, M., Larsson, A., Schaal, W., Novella, J., Tommaso, P. D., Notredame, C., Moreno, P., Khoonsari, P. E., Herman, S., Kultima, K., and Lampa, S. Peer J.
The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018) by Harris, N., Wiencko, H., Chapman, B., Cock, P. J ., Hokamp, K., Lapp, H., Fields, C., and Greshke Tzovaras, B. F1000 Research.
sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data by Pogorelcnik, R., Vaury, C., Pouchin, P., Jensen, S., and Brasset, E. Mobile DNA.
Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study by Vanneste, K., Garlant, L., Broeders, S., Van Gucht, S., and Roosens, N. H. BMC Bioinformatics.
Implementation of a Reproducible, Accessible and Transparent RNA-seq Bioinformatics Pipeline within the Galaxy Platform by Ali, T., Kim, B., Lijeron, C., Dong, C., Wultsch, C., and Krampis, K. Journal of Computer Science & Systems Biology.
New Galactic Blog Posts
There are three new Galactic Blog entries:
- Hybrid training delivers online participatory training to far-reaching venues, by Christina Hall
Tutorial of the Month: Maria Doyle selected "From peaks to genes", by Bérénice Batut
- This is the first of a new monthly series about GTN Tutorials.
- Contributor of the Month: Yvan Le Bras, By Björn Grüning
The dark energy* of irreproducible research is threatening the science universe! Please help the Galaxy expand!
- Bioinformatics Cloud Architect, EMBL-EBI, Hinxton, United Kingdom
- 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 software engineers and postdocs at Johns Hopkins, Baltimore, Maryland, United States
Have a Galaxy-related opening? Send it to firstname.lastname@example.org and we'll put it in the Galaxy News feed and include it in next month's update.
Public Galaxy Server News
Public Galaxy Servers is becoming something ... more
In October the venerable Public Galaxy Server list and the relative upstart Galaxy Services list will be replaced with a unified directory that includes public servers, cloud services, and VMs and containers that support Galaxy.
Here's what's new:
The Molecular Property Diagnostic Suite for Diabetes Mellitus (MPDS-DM) is a Galaxy web portal that serves as an open access data repository containing available chemical and gene-level information on diabetes. MPDS-DM tools allow users to identify, explore, and characterize drug:gene relationships.
See the MPDS-DM directory entry for more.
CRAVAT-P is a proteomic extension of the Cancer-Related Analysis of VAriants Toolkit (CRAVAT) developed for the Galaxy-P bioinformatics platform. CRAVAT-P exists as a downstream analysis suite for peptide variants. Current support is tailored towards workflows that generate peptide sequences mapped to genomic locations.
See the CRAVAT-P directory entry for more.
Public Servers/Resources in Publications
We tag papers that use, mention, implement or extend public Galaxy servers, services and other resources. Here are the counts for the past month's publications:
|1||[>Genomic Hyperbrowser](https://www.zotero.org/groups/1732893/galaxy/tags/>Genomic Hyperbrowser)||1||>GenOuest||1||[>Globus Genomics](https://www.zotero.org/groups/1732893/galaxy/tags/>Globus Genomics)||1||>GVL-MEL|
|1||>Hunter||1||[>LAPPS Grid](https://www.zotero.org/groups/1732893/galaxy/tags/>LAPPS Grid)||1||>MPDSDM||1||>Orione|
Tool Shed contributions in September 2018.
New additions to the Galaxy Community.
The Genomics Virtual Lab (GVL) 4.4.0 has been released. The GVL is a comprehensive data analysis workbench that comes as a complete package with a variety of pre-installed and configured software (Galaxy, RStudio, Jupyter) coupled with cloud compute infrastructure. This latest release includes an upgrade of Galaxy to version 18.05, allows overridable Galaxy Configuration, and has many tools updraged to their latest revision.
See the GVL 4.4.0 release note for more.
Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. See GitHub for details on this release.
galaxy-lib 18.5.14 - 18.9.1
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.
This month's updates are about mulled, Conda, and CWL tools.
And the rest ...
Other Galaxy packages that didn't have a release in the past month can be found on GitHub.
The Galaxy Training Network is starting a Community for Galaxy Instructors. This group will share best practices for giving Galaxy workshops and provide support for new instructors to get involved with Galaxy Training! Catch the first meeting October 5th, details here.