October 2017 Galaxy News
Welcome to the October 2017 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 firstname.lastname@example.org.
What do fall foliage, pumpkin beer, and Halloween have in common? October! Or, we should say Hacktoberfest. From Oct 1st through Oct 31st, Hacktoberfest is a celebration of open source coding organized by Digital Ocean and GitHub. This is a great opportunity to get involved with a project and get some help along the way. Plus, if you issue 4 pull request during the month, you get a limited edition t-shirt! Any project on GitHub can participate simply by creating and tagging issues with Hacktoberfest tag. If you'd like to participate on a Galaxy-related project, see the Galaxy Hacktoberfest dashboard.
The Galactic and Stellar publications added in September were:
- wft4galaxy: a workflow testing tool for galaxy
- Marco Enrico Piras, Luca Pireddu, Gianluigi Zanetti, Bioinformatics, btx461, doi:10.1093/bioinformatics/btx461
- Satellite DNA: An Evolving Topic
- Manuel A. Garrido-Ramos, Genes 2017, 8(9), 230; doi:10.3390/genes8090230
- mmquant: how to count multi-mapping reads?
- Matthias Zytnicki, BMC Bioinformatics, 201718:411 doi:10.1186/s12859-017-1816-4
- Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms
- Nico J. Claassens, Melvin F. Siliakus, Sebastiaan K. Spaans, Sjoerd C. A. Creutzburg, Bart Nijsse, Peter J. Schaap, Tessa E. F. Quax, John van der Oost, PLOS One, Published: September 13, 2017, doi:10.1371/journal.pone.0184355
- GWIPS-viz: 2018 update
- Audrey M. Michel, Stephen J. Kiniry, Patrick B. F. O’Connor, James P. Mullan, Pavel V. Baranov, Nucleic Acids Research, gkx790, doi:10.1093/nar/gkx790
- Big Data for Infectious Diseases Surveillance and the Potential Contribution to the Investigation of Foodborne Disease in Canada
- Cheryl Waldner, National Collaborating Centre for Infectious Diseases (NCCID)
- A Single TCF Transcription Factor, Regardless of Its Activation Capacity, Is Sufficient for Effective Trilineage Differentiation of ESCs
- Steven Moreira, Enio Polena, Victor Gordon, Solen Abdulla, Sujeivan Mahendram, Jiayi Cao, Alexandre Blais, Geoffrey A. Wood, Anna Dvorkin-Gheva, Bradley W. Doble, Cell Reports, Volume 20 , Issue 10 , 2424 - 2438, doi:10.1016/j.celrep.2017.08.043
- Antigen receptor sequencing of paired bone marrow samples shows homogeneous distribution of acute lymphoblastic leukemia subclones
- Prisca M.J. Theunissen, David van Zessen, Andrew P. Stubbs, Malek Faham, Michel Zwaan, Jacques J.M. van Dongen, Vincent H.J. Van der Velden, Haematologica, August 2017 : haematol.2017.171454; doi:10.3324/haematol.2017.171454
108 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in September.
We also added tags to papers that reference, use, or implement a Galaxy Public Server. See below for this list.
There are a plenitude of Galaxy related events coming up in the next few months:
See the Galaxy Events Google Calendar for details on other events of interest to the community.
The Galaxy is expanding! Please help it grow.
- 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
- Implémentation d’outils d’analyse et de visualisation de variations structurales et génomes mosaïques, IRD (Institut de Recherche pour le Développement), Montpellier, France
- Metabarcoding, analyses écologiques et statistiques de paleocommunautés de protistes de l’écosystème côtier, IFREMER DYNECO/Pelagos, Brest, France
- Bioinformatics Research Associate, Huttenhower Lab, Harvard School of Public Health, Boston, Massachusetts, United States
As mentioned above, as part of the move to Zotero, we have started tagging papers that use, mention, implement or extend public Galaxy Servers with the server name. Here are the counts for September's papers.
- Edit marker or channel names in FCS files – fix any typo to make your FCS files compatible for multi-files analysis
- Merge and downsamples FCS files – create an aggregate of your files to identify patterns or populations in your sample set.
- Generate a Self-Organizing Map using FlowSOM,
- Compare individual files to the tree, or
- Compare samples to one another using the FlowSOM tree.
- Visualize your data with an interactive heatmap generated by Clustergrammer.
The ImmPort Project is also seeking feedback on how people use the ImmPort Galaxy server. If you are a user then please let them know. (And if you aren't a user and you do flow cytomety then give ImmPort Galaxy a look.)
Codon Harmonizer supports generating codon harmonized variants of gene sequences for heterologous expression. This tool-publishing server comes from the Laboratory of Microbiology at Wageningen University and Research
From Claassens et al.:
"...different codon usage variants significantly improved production of some of the tested proteins. However, not a single algorithm performed consistently best for the membrane-integrated production of the 6 tested proteins. In conclusion, for improving heterologous membrane protein production in E. coli, the major effect is accomplished by transcriptional tuning. In addition, further improvements may be realized by attempting different codon usage variants, such as codon harmonized variants, which can now be easily generated through our online Codon Harmonizer tool."
See the Codon Harmonizer page for more.
A Pulsar update was released in September. Pulsar is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the results are transferred back to the Galaxy server - eliminating the need for a shared file system.
This release adds several features and 4 bug fixes.
This set of revisions includes:
- Latest updates from the upcoming 17.09 release - including updating the default target Conda version and fixes for module resolution.
- Updated CWL utilities.
- Remove command lint check that is no longer valid.
- Bring in various Galaxy updates including numerous Conda fixes and changes (thanks to @nsoranzo.
- Improved error handling when parsing tool reStructuredText (thanks to @erasche).
See GitHub for details.
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 0.10.0.
Command-line utilities to help with managing users, data libraries and tools in a Galaxy instance, using the Galaxy API via the BioBlend library.
CAVEAT nebulizer is still a work in progress; please exercise caution when attempting irreversible operations especially against production Galaxy instances (for example when creating users or data libraries).
CloudBridge aims to provide a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. It is currently under development and is in an Alpha state.
Other packages that have been released in the prior 4 months.
The Galaxy Docker project has seen a new release, following Galaxy 17.05. Major features are an additional Docker compose setup with SLURM and HT-Condor deployments, BioContainers integration and much more automatic testing.
- The Galaxy Docker Project has reached more than 23k downloads on Dockerhub - not counting quay.io and all flavors
- From John Chilton:
A new release of Galaxy CloudMan is available on the Amazon Web Services cloud infrastructure. This release includes Galaxy 17.05, an updated tool list, and Slurm configuration changes to improve job performance. To get started, visit https://beta.launch.usegalaxy.org/ or take a look at the Getting Started guide.
Technically, the all-new Galaxy CloudLaunch service has been in public beta since February but keep in mind that it will replace the current CloudLaunch service eventually so give it a try and let us know how it performs for you.
Other Galaxy packages that haven't had a release in the past four months can be found on GitHub.
- From Stephen Ficklin
- Tripal Galaxy in Drupal
- Video: MSI Tutorial: NGS Galaxy QC (QC of Illumina Data using Galaxy), 2017/07/25. Tutorial Organizer: Lauren Mills