August 2014 Galaxy Update
Welcome to the august 2014 Galaxy Update, a monthly summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.
The Galaxy Update is going out a few days early this month because the usual release date is during GCC2014.
Events
GCC2014 Report
2014 Galaxy Community Conference (GCC2014) was held June 30 through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States. It was preceded by by the first ever GCC Hackathon.
Videos of and slides for presentations and Lightning Talks, PDFs of Posters, material for Training Day Sessions, and writeups of BoFs are now all online. There are also several meeting reports now available on the web.
Feedback has been very positive (see below for some of it), and we would like to thank absolutely everyone for making this such a successful meeting.
GCC2014 by the numbers
| Measure | Value | Question | No | Yes, but ... | Yes | |||
|---|---|---|---|---|---|---|---|---|
| Total Participants | 214 | Would you recommend future Galaxy events to others? | 2% | 3% | 95% | |||
| Training Day Participants | 207 | |||||||
| Hackathon Participants | 40 | |||||||
| Videos, slides, posters, exercises, ... | 120+ | Question | Not at all | Below Average | Average | Above Average | Exceptional | |
| Talks | 26 | How useful was the main meeting? | 0% | 0% | 12% | 56% | 32% | |
| Posters | 30 | Was the main meeting well run and organized? | 0% | 0% | 2% | 51% | 47% | |
| Lightning Talks | 15 | |||||||
| Training Day Sessions | 15 | Did the main meeting meet your expectations? | 0% | 0% | 10% | 55% | 35% | |
| BoFs | 6 | |||||||
GCC2015: Norwich, United Kingdom, 6-8 July 2015
We are pleased to announce that the 2015 Galaxy Community Conference (GCC2015) will be held at The Sainsbury Laboratory in historic Norwich, United Kingdom. Norwich is a center of biological research and is home to The Sainsbury Laboratory, The John Innes Centre, The Genome Analysis Centre (TGAC), and The University of East Anglia.
GCC2015 will likely again feature a hackathon, copious training day sessions and topics, posters, birds-of-a-feather sessions, talks, lightning talks, the best darn networking opportunities, and the possible return of an onsite pub. As at past GCC's we will again strive to keep registration costs low, and to offer affordable housing options.
GCC2015 will be held 6-8th July, 2015, which is just before ISMB/ECCB 2015 in Dublin. More details will be announced through Galaxy channels as we know them.
Hope to see you in Norwich!
Galaxy @ ISMB and BOSC 2014 Slides and Posters
Slides and posters for 9 Galaxy related presentations at ISMB and BOSC 2014 this year are now available online too. There's also an interesting writeup of the Bioinfo-Core Workshop including Core on a Budget vs Enterprise and Using pipelines within a core.
Other Events
Over the rest of the few months there are many Galaxy related events in Brisbane, Rio de Janeiro, Rennes, and Melbourne. Galaxy will also be at ECCB'14/JOBIM in Strasbourg, and there is Swiss-German Galaxy Tour in the fall. See the Galaxy Events Google Calendar for details on other events of interest to the community.
New Papers
53 papers were added to the Galaxy CiteULike Group in July. Some papers that may be particularly interesting to the Galaxy community:
- HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization, by Paulsen, et al., Bioinformatics (2014) 30 (11): 1620-1622. doi: 10.1093/bioinformatics/btu082
- Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system, by Todd H. Oakley, Markos A. Alexandrou, Roger Ngo, et al., BMC bioinformatics, Vol. 15, No. 1. (2 July 2014), 230, doi:10.1186/1471-2105-15-230
- QSAR-Based Models for Designing Quinazoline/Imidazothiazoles/Pyrazolopyrimidines Based Inhibitors against Wild and Mutant EGFR, by Jagat S. Chauhan, Sandeep K. Dhanda, Deepak Singla, Subhash M. Agarwal, Gajendra P. S. Raghava, Open Source Drug Discovery Consortium, PLoS ONE, Vol. 9, No. 7. (3 July 2014), e101079, doi:10.1371/journal.pone.0101079
- A Survey of Approaches and Frameworks to Carry Out Genomic Data Analysis on the Cloud, by Philip C. Church, Andrzej Goscinski, in "Cluster, Cloud and Grid Computing (CCGrid)", 2014 14th IEEE/ACM International Symposium on (May 2014), pp. 701-710, doi:10.1109/ccgrid.2014.127
- Physiolyze: A Galaxy-based web service for Heart Rate Variability analysis with online processing, by Andrea Bizzego, Marco Mina, Calogero Zarbo, Gianluca Esposito, Cesare Furlanello, in "Cardiovascular Oscillations (ESGCO)," 2014 8th Conference of the European Study Group on (May 2014), pp. 97-98, doi:10.1109/esgco.2014.6847537
The new papers were tagged in many different areas:
| # | Tag | # | Tag | # | Tag | # | Tag | |||
|---|---|---|---|---|---|---|---|---|---|---|
| 3 | Cloud | - | Project | 8 | Tools | 6 | UsePublic | |||
| 1 | HowTo | 3 | RefPublic | - | UseCloud | - | Visualization | |||
| 4 | IsGalaxy | 2 | Reproducibility | 1 | UseLocal | 15 | Workbench | |||
| 26 | Methods | 2 | Shared | 8 | UseMain |
Who's Hiring
The Galaxy is expanding! Please help it grow.
- Computational Science Developer I, Cold Spring Harbor Laboratory (CSHL), New York, United States
- Galaxy Platform Development Officer, The Genome Analysis Centre (TGAC), Norwich, United Kingdom. Closes 12 August.
- Bioinformatician position at Xenbase, University of Calgary.
- Experimental Officer in Bioinformatics, NERC Metabolomics Facility, University of Birmingham, UK
- Statistical Genomics Postdoc opening in the Makova lab at Penn State
- The Galaxy Project is hiring software engineers and post-docs
Got 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 Public Servers
One new public Galaxy server was added to the published list in July:
IM-PET
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Link:
-
Domain/Purpose:
- IM-PET makes genome-wide predictions of enhancer-promoter (EP) interactions by integrating multiple types of genomics data.
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Comments:
- See He B et al. Global view of enhancer-promoter interactome in human cells[J] . Proceedings of the National Academy of Sciences of the United States of America, 2014.
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User Support:
- Email to Bing He or contact the Tan Lab
- Quotas:
-
Sponsor(s):
Galaxy Distributions
- June 2, 2014 Galaxy Distribution
- Corresponding version of the ToolShed
- BioBlend 0.4.3 was released on April 11, 2014.
- The most recent version of CloudMan was released in January 2014.
Security Vulnerability
A security vulnerability was recently discovered by Inge Alexander Raknes that would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability was in a method that uses Python "pickle" functionality to decode state information from tool forms. Because pickles can be used to instantiate arbitrary Python objects, tool states could be constructed to exploit this vulnerability.
Because this vulnerability allows for arbitrary code execution, administrators are strongly encouraged to apply this fix immediately. See this posting for details on how to fix this problem.
Galaxy Community Hubs
| Share your experience now |
There were no new Log Board or Deployment Catalog entries in July! Eek! Please don't let this happen again!
The Community Log Board and Deployment Catalog Galaxy community hubs were launched last your. If you have a Galaxy deployment, or experience you want to share then please publish them this month.
ToolShed Contributions
... we didn't get there this month. Look for a double helping of tools in the September newsletter.
Other News
- Semi-annual update of the Galaxy Project Statistics page.
- New Galaxy training resource: UCDavis Genome Center Bioinformatics Core June 2014 Workshop: Slides, exercises, datasets + an AMI!
- New Expanded RNA-Seq Galaxy and Galaxy NGS 101: Synechocystis remix using a custom genome tutorials by Cynthia Gibas at GenomeIntelligence.