February 2014 Galaxy Update
Welcome to the February 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.
42 papers were added to the Galaxy CiteULike Group in January. Some papers that may be particularly interesting to the Galaxy community:
- CGtag: Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy, by Hiltemann, et al., GigaScience, Vol. 3, No. 1. (2014), 1, doi:10.1186/2047-217x-3-1
- PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis, by Chen, et al., Genome biology, Vol. 15, No. 1. (22 January 2014), R18, doi:10.1186/gb-2014-15-1-r18
- Oqtans: The RNA-seq Workbench in the Cloud for Complete and Reproducible Quantitative Transcriptome Analysis, by by Sreedharan, et al., Bioinformatics (Oxford, England) (11 January 2014), btt731, doi:10.1093/bioinformatics/btt731
- Learn2Mine: Data Science Practice and Education through Gameful Experiences, International Journal of e-Education, e-Business, e-Management and e-Learning, by Turner, *et al.,*Vol. 4, No. 3. (2014), doi:10.7763/ijeeee.2014.v4.338
How those papers were tagged:
The Galaxy is expanding! Please help it grow.
- Postdoctoral position in genomics/bio-informatics (NGS) at University of Rennes 1 (France)
- Post-doctoral Data analyst / Bioinformatician position for high-throughput data analysis : Paris, France
- Statistical Genomics Postdoc opening in the Makova lab at Penn State
- The Galaxy Project is hiring software engineers and post-docs, including positions at George Washington University.
GCC2014: June 30 - July 2, Baltimore
Registration opens February 10
Early registration will open February 10. The Training Day schedule will also be posted at that time. The organizers are currently contacting potential instructors and building the schedule. Thanks to everyone who took the time to nominate and vote on Training Day topics.
Training Day is an opportunity to learn about all things Galaxy including using Galaxy, deploying and managing Galaxy, extending Galaxy, and Galaxy internals. There will be 4 parallel tracks, each with 3 sessions, with each of those sessions two and half hours long. That's 12 sessions and 30 hours of workshop material.
In 2014 we are also adding non-sponsor exhibit spaces in addition to the sponsor exhibits. This will significantly increase the size of the exhibit floor. Please contact the Organizers if your organization would like to have an exhibit space at GCC2014.
Galaxy Australasia Workshop 2014 (GAW 2014)
The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.
The Galaxy Australasia Workshop is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne. GAW 2014 will also include poster session, keynote speakers.
Registration is open. Registration is also free, but space is limited.
Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit an abstract and brief one-paragraph bio by February 15th, 2014. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.
GAW 2014 will be held in Melbourne, Australia on 24 and 25th March 2014. The first day (Monday) will be in Clayton, next to the Australian Synchrotron. For the 2nd day (Tuesday) we will move downtown the Melbourne Convention Centre, the venue for the Computational and Simulation Sciences and eResearch.
GMOD Malaysia 2014
February 26-28, 2014, Kuala Lumpur, Malaysia.
GMOD Malaysia 2014 offers an introduction to, and training in, the bioinformatics software offered by the Generic Model Organism Database project (http://gmod.org). Over three days, participants will learn about GMOD's free, open-source tools for visualising, storing, and disseminating genetic and genomic data. These include: '''Galaxy''', the GBrowse and JBrowse genome browsers, InterMine data warehouse (a frequent Galaxy data source), MAKER and MAKER-P genome annotation pipelines, Tripal website generator and database interface and the Chado database schema
Instruction is by experienced instructors and developers with deep knowledge of the tools and their applications. By the end of the course, participants will have hands-on experience of setting up and using core components needed for a modern genomics project.
GMOD Malaysia 2014 is made possible by the generous support of the National Evolutionary Synthesis Center (NESCent) and the NESCent Ambassador program. NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent supports research and education across disciplinary, institutional, geographic, and demographic boundaries. The NESCent Ambassador Program is NESCent’s primary international outreach program, and is supported by a three-year grant from the NSF.
Other Eventshttp://bit.ly/gxycal) for details on other events of interest to the community.
New Public Servers
Several new servers were added to the list of publicly accessible Galaxy servers last month.
Genomics Virtual Lab
- Link: Galaxy Tut
- Domain/Purpose: Small Galaxy for Training purposes. Loaded with Histories and Tools for Next Gen Sequencing tutorials.
- Comments: Follow tutorials at GVL Learn and use Galaxy Tut
- User Support: [Email](mailto:help AT uq DOT edu DOT au)
- Quotas: 50Gb
- Sponsor(s): Genomics Virtual Lab by University of Queensland, Victorian Life Sciences Computation Initiative, Queensland Facility for Advanced Bioinformatics, and Garvan Institute
CTMM-TraIT Demo Galaxy
- CTMM-TraIT Demo Galaxy
- "CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy" by Hiltemann, et al., GigaScience 2014, 3:1 doi:10.1186/2047-217X-3-1
- Domain/Purpose: Implements CGATools, the Complete Genomics open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files in a Galaxy instance called CGtag (Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy).
- Comments: Includes two Galaxy Pages, and example data and public workflows to support themL
- User Support: Please email questions to [Saskia Hiltemann](mailto:s DOT hiltemann AT erasmusmc DOT nl)
- Sponsor(s): This Galaxy Server was set up by the Netherlands Bioinformatics Center (NBIC) and is maintained by CTMM-TraIT, running at SurfSARA high-performance cloud.
- "PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis" by Chen, et al., Genome Biology, 2014, 15:R18 doi:10.1186/gb-2014-15-1-r18
- Domain/Purpose: This server hosts custom tools developed by members of the Quantitative Biomedical Research Center @ University of Texas Southwestern for statistical analysis of various High Throughput Sequencing experiments. This server features PIPE-CLIP.
- Comments: The QBRC galaxy server tools are constantly being updated. Please contact authors for more details regarding use.
- User Support: Web form
- Sponsor(s): Quantitative Biomedical Research Center @ UT Southwestern
January 2014 CloudMan Release
An update to Galaxy CloudMan was released in January. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.
This update brings a large number of updates and new features. See the release announcement for the list. For more details on the new features, see the the CHANGELOG and for even more details see, all 103 commit messages from 4 contributors.
Galaxy Community Hubs
New Galaxy Deployment Catalog entries:
bringing the number of deployment descriptions to 10.
New Community Log Board entries
bringing the number of log entries to 12.
New Repositories in the Galaxy Project ToolShed
- prims_metabolomics: Metabolomics module of Plant Research International's Mass Spectrometry (PRIMS)
- diffbind: Differential Binding Analysis of ChIP-Seq peak data (web site)
- The devteam created 60 new repos for:
bowtie2, ccat, clustalw, dwt_cor_ava_perclass, dwt_cor_avb_all, dwt_ivc_all, dwt_var_perclass, dwt_var_perfeature, express, fastq_combiner, fastq_filter, fastq_groomer, fastq_manipulation, fastq_masker_by_quality, fastq_paired_end_deinterlacer, fastq_paired_end_interlacer, fastq_paired_end_joiner, fastq_paired_end_splitter, fastq_stats, fastq_to_tabular, fastq_trimmer, fastq_trimmer_by_quality, fastqc, fastqtofasta, filter_transcripts_via_tracking, find_diag_hits, freebayes_wrapper, gi2taxonomy, gmaj, lca_wrapper, macs, package_bowtie_0_12_7, package_bowtie2_2_1_0, package_ccat_3_0, package_clustalw_2_1, package_express_1_1_1, package_fastqc_0_10_1, package_galaxy_utils_1_0, package_ghostscript_9_10, package_macs_1_3_7_1, package_r_2_15_0, package_readline_6_2, package_sicer_1_1, package_taxonomy_1_0_0, package_tophat_1_4_0, package_tophat2_2_0_9, package_weblogo_3_3, poisson2test, sicer, t2ps, t2t_report, tabular_to_fastq, tophat, tophat_fusion_post, tophat2, vcf_annotate, vcf_extract, vcf_filter, vcf_intersect,and
Galaxy is now at Johns Hopkins and GWU (and Penn State!)
In case you haven't heard, the former Emory University contingent of the Galaxy Team went north this month to Baltimore - it's warmer there (at least this week), where James Taylor is now an Associate Professor in the Johns Hopkins Biology and Computer Science Departments. Jeremy Goecks, also formerly of the Emory University contingent is now an Assistant Professor of Computational Biology at George Washington University in the Washington DC area.
None of these moves should be particularly noticeable to the Galaxy community. We didn't lose anyone in these transitions, and in fact we are still hiring, but now at three universities instead of two.
- GVL Galaxy Launch video: How to open your own private Galaxy bioinformatics server using the Genomics Virtual Lab interface to the NeCTAR Australian research cloud. Based on the guide at GVL.
- Galaxy RNA-Seq Analysis Tuxedo protocol video: Video in Korean; slides in English
- bioblend 0.4.2 released: CloudMan and Galaxy API library
- Biocuration 2014 Workshops & Satellites announced, including Data Curation in the age of hyperabundance.