The March 2015 Galaxy News
Welcome to the March 2015 Galaxy Update, a 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.
New Papers
82 new papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in February. Some highlights:
- Multi-omic data analysis using Galaxy Jorrit Boeke, John M Chilton, Ira R Cooke, Peter L Horvatovich, Pratik D Jagtap, Lukas Käll, Janne Lehtiö, Pieter Lukasse, Perry D Moerland & Timothy J Griffin, Nature Biotechnology, Vol. 33, No. 2. (6 February 2015)
- Online Resources for Genomic Analysis Using High-Throughput Sequencing Daniel Blankenberg, James Taylor, Anton Nekrutenko, Cold Spring Harbor Protocols (05 February 2015), doi:10.1101/pdb.top083667
- Selected Approaches and Frameworks to Carry out Genomic Data Analysis on the Cloud Philip Church, Andrzej Goscinski, Scalable Computing: Practice and Experience, Vol. 16, No. 1. (07 February 2015), doi:10.12694/scpe.v16i1.1058
- Data Interlocking: Coupling Analytics to the Data Yousef Kowsar, Harriet Dashnow, Andrew Lonie, in Utility and Cloud Computing (UCC), 2014 IEEE/ACM 7th International Conference on (December 2014), pp. 696-701, doi:10.1109/ucc.2014.113
- A Quick Guide for Building a Successful Bioinformatics Community Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg, PLoS Computational Biology, Vol. 11, No. 2. (5 February 2015), e1003972, doi:10.1371/journal.pcbi.1003972
- Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828 Timothy D Read, Robert A Petit III, Sandeep J Joseph, Md T Alam, Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S Vuong, Chad P Haase, Harry Webb, Alistair D. M. Dove, PeerJ PrePrints 3:e1036 doi:10.7287/peerj.preprints.837v1
- Reproducibility and reusability of genome assembly evaluation Sabba Ifzal, MS Thesis, University of Oslo
The new papers were tagged with:
| # | Tag | # | Tag | # | Tag | # | Tag | |||
|---|---|---|---|---|---|---|---|---|---|---|
| 4 | Cloud | 3 | Project | 1 | Tools | 13 | UsePublic | |||
| 2 | HowTo | 7 | RefPublic | - | UseCloud | - | Visualization | |||
| 2 | IsGalaxy | 6 | Reproducibility | 2 | UseLocal | 20 | Workbench | |||
| 42 | Methods | 1 | Shared | 8 | UseMain |
UseGalaxy.org Update
A refresh of UseGalaxy.org has started. It includes
- New versions of Bowtie2, bwa-mem, Picard, BAMTools, FastQC, ....
- New look and feel for tool forms
- New Scratchbook features
- New Charts functionality
All of these are described in the new Galaxy Screencast GXYCast1: 2015. Look for more updates coming soon.
Events
GCC2015: 6-8 July, Norwich UK
The 2015 Galaxy Community Conference (GCC2015) is the Galaxy community's annual gathering of users, developers, and administrators. Previous GCC's have drawn over 200 participants, and we expect that to happen again in 2015. GCC2015 is being hosted by The Sainsbury Lab in Norwich, UK, immediately before BOSC and ISMB/ECCB in Dublin.
There are a lot of events going on at GCC2015, including:
- Code Hackathon, 4-5 July
- Data Wrangling Hackathon, 4-5 July (new)
- Training SunDay, 5 July (new)
- Training Day, 6 July
- GCC Meeting, 7-8 July
Code Hackathon
An intense two-day hands-on collaboration to develop working code that is useful to the Galaxy community. If you know how to code, and want to contribute to one of the most successful open source projects in the life sciences, then please consider attending. See the Code Hackathon home page for more.
Data Wrangling Hackathon
An intense two-day hands-on collaboration to develop cutting edge analysis pipelines that are useful to the Galaxy community. If you know data analysis, we would love to have you here to help us beat back those seemingly unsurmountable analysis challenges. See the Data Wrangling Hackathon home page for more.
Training SunDay
Something new for GCC2015 is Training SunDay, an additional day of training offered the day before its older sibling Training Day, and featuring a single track with the most in-demand topics. You can attend both Training Days, or just one. Training SunDay features these three topics:
These three topics are also offered on Monday as well. You can register for one or both Training Days.
Training (Mon)Day
The schedule for Training Day, Monday, 6 July is available. Training Day featuring five parallel tracks, each with three, two and a half hour workshops. There are topics on using Galaxy, interacting with it programmatically, and deploying, administering, and extending Galaxy. No matter what you do with Galaxy, there are workshops for you.
Early Registration opens in March
Early registration (save heaps) will open in March. Early registration is very affordable and starts at less than £40 per day for students and postdocs. If you work in data-intensive life science research, then it is hard find a meeting more relevant than GCC2015. We look forward to seeing you there.
Abstract Submission is Now Open
Abstract submission for Oral and Poster Presentations at the 2015 Galaxy Community Conference (GCC2015) is now open.
Abstract submission for oral presentations closes 10 April, while poster submission closes 1 May. Poster authors will be notified of acceptance status within two weeks of submission, while oral presentation authors will be notified no later than 24 April. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.
We are pleased to announce that again in 2015, any oral or poster presentation will also be eligible for consideration for publication in the GigaScience "Galaxy: Data Intensive and Reproducible Research" series (first announced for GCC2013). GigaScience is pleased to offer a 15% discount on article publishing charges for accepted papers from GCC2015.
GCC2015 Sponsorships
We are pleased to announce that BioTeam will again be a Gold Sponsor for this annual event. This is the third year in a row that BioTeam has been a GCC Gold Sponsor.
Call for Sponsors
The 2015 Galaxy Community Conference (GCC2015) is now accepting Sponsorships. Your organisation can play a prominent part in the Galaxy community by sponsoring GCC2015. Sponsorship is an excellent way to raise your organization’s visibility.
Several sponsorship levels are available, including two levels of premier sponsorships that include presentations. Premium sponsorships are limited, however, so you are encouraged to act soon.
Please let the organisers ([gcc2015-org AT lists DOT galaxyproject DOT org](mailto:gcc2015-org AT lists DOT galaxyproject DOT org)) know if you are interested in helping make this event a success.
RNA-Seq and ChIP-Seq Analysis with Galaxy, UC Davis, March 23-26
A hands-on, 4 day workshop on RNA-Seq and ChIP-Seq Analysis with Galaxy will be held at the UC Davis Bioinformatics Core in Davis, California, United States, March 23-26. There are just a few slots left.
February GalaxyAdmins Meetup
Video and slides from the first GalaxyAdmins meetup of 2015 are now available online.
Hans-Rudolf Hotz also lead a short discussion on GalaxyAdmins direction.
GalaxyAdmins is a special interest group for Galaxy community members who are responsible for Galaxy installations. Our next meetup will be in April.
Fall 2014 Questionnaire Summaries
A summary of both the user and admin/developer 2014 Galaxy Community Questionnaires was presented by Dave Clements. A summary of the admin/devel questionnaire is now available online.
Gravity
Nate Coraor introduced Gravity, a process manager (supervisor) for Galaxy servers.
Other Events
There are upcoming events in 7 countries on 4 continents. See the Galaxy Events Google Calendar for details on other events of interest to the community.
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Designates a training event offered by GTN member(s) |
Who's Hiring
The Galaxy is expanding! Please help it grow.
- Developer / bioinformatician at the University Center for Information Technology (USIT) at the University of Oslo
- Computational Metabolomics Professor, Penn State University, Pennsylvania, United States
- Software Developer for the Refinery Team, Boston, Massachusetts, United States
- Bioinformatics scientist/engineer for RNA bioinformatics and next-generation sequencing, MDC Berlin-Buch
- Searching for bioinformaticians, post-docs, PhD students and software engineers in Freiburg, Germany at Max Planck Institute of Immunobiology and Epigenetics, and the Bioinformatics Group at the University of Freiburg
- 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 servers was added in February:
Whale Shark
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Link:
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Domain/Purpose:
- "Dedicated to the analysis of whale shark (Rhincodon typus) genome."
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Comments:
- See: Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828, Read TD, Petit III RA, Joseph SJ, Alam MT, RW, Ahmad M, Bhimani R, Vuong JS, Haase CP, Webb H, Dove ADM. (2015). PeerJ PrePrints 3:e1036 https://doi.org/10.7287/peerj.preprints.837v1
- User Support:
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Quotas:
- Max file size to upload: 2 GB
- For registered users, you have a disk quota of 50GB and a job walltime of 24 hours.
- For anonymous users, you have a disk quota of 50MB and a job walltime of 30 minutes.
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Sponsor(s):
- "The whale shark genome project was made possible by financial and other support of Georgia Aquarium and its guests, and by a completion grant from The Coca Cola Company."
Galaxy Community Hubs
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| Share your training resources and experience now | Share your experience now |
Two new Community Log Board entires were added in February:
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FTP upload to Galaxy using ProFTPd and PBKDF2
- ProFTPd implemented using PBKFD2 protocol for encryption, by Peter Briggs
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Instalando um servidor do Galaxy Project
- Portuguese Galaxy Documentation, by Léo Biscassi
Galaxy GitHub
Galaxy has moved its source from Bitbucket to GitHub. The development of Galaxy takes place there from now on.
However, the Bitbucket repositories are still the official source for deployment until we polish the process.
More information available in Develop/SourceCode.
Releases
Galaxy 2015-01-13 Distribution
The most recent Galaxy release was the 2015-01-13 distribution. This addressed several critical security vulnerabilities, added IPython integration, and included a Tool Form Upgrade for Beta Testing.
Planemo 0.5.0
There were several releases of Planemo in February. Among many other new features, it is now install-able from PyPI and contains a new command to assist in bootstrapping new tools.
BioBlend
BioBlend v0.5.2 was released in October. BioBlend is a python library for interacting with CloudMan and the Galaxy API. In January the BioBlend source was moved to the galaxyproject Github account.
CloudMan and blend4j
New versions of CloudMan, and blend4j were released in August.
ToolShed Contributions
Galaxy Project ToolShed Repos
There was no shortage of new ToolShed repositories in February, but there was a shortage of time to describe them. Look for a double batch of new tools next month.