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GalaxyUpdates/2015_08

The August 2015 Galactic News!

Galaxy Updates

Welcome to the August 2015 Galactic News, a summary of what is going on in the Galaxy community. It's been, and will be, a busy few months. If you have anything to include in the September News, please send it to Galaxy Outreach <outreach AT galaxyproject DOT org>.

Events

GCC2015 Report

GCC2015

The 2015 Galaxy Community Conference (GCC2015) was held 4-8 July 2015, in Norwich, UK. GCC2015 was hosted by The Sainsbury Lab in Norwich, UK. By all measures, the meeting was a tremendous success.

GCC2015 registrations reached an all-time high, and GC2015 featured more events than any previous GCC:

The GCC2015 Organising Committee would like to thank the Scientific Committee, Coding Hackathon Organisers, Data Wrangling Hackathon Organisers, Conference Sponsors, BoF Organisers, Training Instructors and absolutely everyone else who contributed to the success of GCC2015.

Which brings us to ...

GCC2016: June 25-29, 2016, Bloomington, Indiana, United States

2016 Galaxy Community Conference

We are pleased to announce that the 2016 Galaxy Community Conference (GCC2016) will be held June 25-29 at Indiana University in Bloomington, Indiana, United States.

GCC2016 is the 7th annual gathering of the Galaxy community. The conference will include keynotes, accepted talks, poster sessions, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. Mark your calendars now. Registration will open in the fall.

And, please help get the word out by posting this announcement at your organization.

If you work in data-intensive biomedical research, there is no better place than GCC2016 to present your work and to learn from others.

August GalaxyAdmins Meetup

GalaxyAdmins meetup August 20
IRIDA

Please join us for the next GalaxyAdmins meetup on August 20 when Aaron Petkau will cover

GalaxyAdmins is a special interest group for Galaxy community members who are responsible for Galaxy installations.


meetup on 23 July 2015

July 2015 Pitagora-Galaxy Meetup

The Pitagora-Galaxy community in Japan had a meetup on 23 July 2015 at the National Institute of Informatics in Tokyo. The discussion is summarized here (in Japanese).


ISMB ECCB 2015
BOSC 2015

Galaxy at ISMB/ECCB and BOSC 2015

BOSC 2015 and ISMB/ECCB 2015 followed immediately after GCC2015 this year, and Galaxy again a significant presence at both.

Slides, posters and videos for most presentations are now available on the Galaxy @ ISMB/ECCB and BOSC 2015 page.

Other Events

http://bit.ly/gxycal

There are upcoming events in four countries on three continents. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Workshop: Extended RNA-Seq analysis RNA-seq data analysis NGS Course Using Galaxy for Analysis of High Throughput Sequence Data  

Date

Topic/Event

Venue/Location

Contact

August 6-7

Workshop: Extended RNA-Seq analysis

Images/Icons/Australia40.png
QFAB, University of Queensland, St Lucia, Australia

Training offered by GTN Member
Mark Crowe

September 7-9

RNA-seq data analysis NGS Course

Images/Icons/Europe40.png
Leiden University Medical Center, The Netherlands

Training offered by GTN Member
BioSB Education <education@biosb.nl>

September 14-18

Using Galaxy for Analysis of High Throughput Sequence Data

Images/Icons/NorthAmerica40.png
UC Davis Bioinformatics Core, Davis, California, United States

Training offered by GTN Member
UC Davis Bioinformatics <bioinformatics.core@ucdavis.edu>

September 15

Towards accessible, reproducible, and transparent research in the life sciences: an innovative open source VRE approach in Western France

Images/Icons/NorthAmerica40.png
HUBbub 2015, Indianapolis, Indiana, United States

Yvan Le Bras

September 21-25

Traitement des données métabolomiques sous Galaxy

Images/Icons/Europe40.png
Station Biologique de Roscoff, France

Training offered by GTN Member
W4M Course Organisers <w4mcourse2015.organisation@sb-roscoff.fr>

October
12-14

Analyse avancée de séquences

Images/Icons/Europe40.png
Bordeaux Bioinformatics Center, University Bordeaux Segalen, France

Email <cfe.contact@cnrs.fr>

November 17-18

Analyse de données RNA-seq sous l’environnement Galaxy

Images/Icons/Europe40.png
PRABI, Lyon, France

Training offered by GTN Member
Email <contact@fc3bio.fr>

December
7-11

Galaxy and the Genomics Virtual Lab

Images/Icons/Australia40.png
BioInfoSummer 2015, University of Sydney, NSW, Australia

Designates a training event offered by GTN Member

Designates a training event offered by GTN member(s)


New Papers

143 new papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in June and July. Highlights include:

The new papers were tagged with:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

8

Cloud

2

Project

11

Tools

11

UsePublic

1

HowTo

6

RefPublic

-

UseCloud

1

Visualization

10

IsGalaxy

5

Reproducibility

6

UseLocal

44

Workbench

57

Methods

3

Shared

16

UseMain


NGS 101 Tutorial Videos are Now Online

Galaxy NGS 101 Videos

The new Galaxy NGS 101 Tutorial was published this spring and introduces a wide range of topics related to analyzing next generation sequencing data with Galaxy. We are happy to announce that videos to accompany this tutorial are now online as well. The 20 videos cover:

  1. Uploading data from your computer

  2. Uploading data from FTP

  3. Uploading data from the Web

  4. Uploading data from EBI SRA

  5. Uploading data from NCBI SRA

  6. QC'ing with FastQC

  7. A quick into to read mapping

  8. Mapping to YOUR reference

  9. Tweaking BAM

  10. Non-diploid variant calling with NVC

  11. Non-diploid varinat calling with FreeBayes

  12. Looking at multiple datasets in IGV

  13. Calling variants with FreeBayes

  14. RNA-Seq: Mapping with TopHat

  15. RNA-Seq: Assembling and quantifying transcripts with CuffLinks

  16. RNA-Seq: Playing with CuffDiff output and Cummerbund to find differentially expressed transcripts

There are also 4 new videos that provide an overview of different sequencing platforms:

The videos join over 60 other videos on the Galaxy Project Vimeo Channel.

Genomic Data Science with Galaxy Launched on Coursera

Genomic Data Science with Galaxy

A Genomic Data Science with Galaxy course was launched on the online teaching platform Coursera in July. The course is part of the Genomic Data Science Specialization. A new session starts every month from now through at least the end of 2015. Coursera courses can be taken for free, or you can pay the course fee and receive a certificate upon completion.

The video lectures for the Galaxy material is on Vimeo.


Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

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.



FingeRprinting Ontology of Genomic variations (FROG)
AGEseq Galaxy @ AspenDB
BioMaS Galaxy
SIFTED
MISSIPPI
70+ Public Galaxy Servers

New Public Galaxy Servers

July was a banner month, with the addition of 5 new publicly accessible Galaxy servers, bringing the list of public servers to over 70.

  1. AB-OpenLab FROG, from CSIR- GENESIS: Genomics and Informatics Solutions for Integrating Biology

    • FingeRprinting Ontology of Genomic variations: FROG fingerprints capture genomic variations at different levels. See the FROG server description for more.

  2. AGEseq Galaxy @ AspenDB, from the Tsai Lab, Warnell School of Forestry and Natural Resources and Department of Genetics, University of Georgia.

    • AGEseq (Analysis of Genome Editing by Sequencing) compares amplicon sequences with expected target sequences and finds insertion/deletion sites in the amplicon sequences. See the AGEseq server description for more.

  3. BioMaS Galaxy from the Istituto Nazionale di Fisica Nucleare

  4. MISSISSIPPI Server from The ARTbio bioinformatics facility of the Institut de Biologie Paris Seine based at the University Pierre & Marie Curie.

    • RNA and small RNA sequencing dataset analysis as well as for epigenetics or metagenomics studies. See the server descriptions for more.

  5. SIFTED from Bulyk Lab, Division of Genetics in the Department of Medicine at Brigham & Women's Hospital and Harvard Medical School

    • Specificity Inference For TAL-Effector Design (SIFTED) is a computational model for predicting the DNA-binding specificity of any Transcription activator-like effector (TALE) proteins. See the server description for more.



Community Committers

Community Committers!

Galaxy now has a formal and open policy for managing the project source code - including for how to add and remove committers. Anyone can issue pull requests and join in the conversation, but committers are trusted to decide how these pull requests are integrated and can participate in formal voting. Read more in (Pull Request 314). Based on their frequent contributions both in terms of code written and contribution to discussions - the Galaxy Project added three new contributors as part of this process. Nicola Soranzo, Björn Grüning, and Eric Rasche are now committers.

Galaxy Community Hubs

Galaxy Training Network

Galaxy Community Log Board

Galaxy Deployment Catalog

Share your training resources and experience now

Share your experience now

Describe your instance now


Three new Community Log Board entries were added in July:

And the new Galaxy NGS 101 set of exercises, and the Galaxy Coursera material were added to the Teaching Resources Directory:


Updated Galaxy Logos

Updated Galaxy Project Logo

Pura Design

You may have noticed in the past two months that an updated Galaxy logo has been slowly appearing on project web sites and presentations. The new logo was created by Petr Kadlec of Pura Design, and it slowly making its way into all Galaxy Project logos. As this happens, they will be added to the Images/GalaxyLogos page.


Releases

BioBlend 0.6.0 and 0.6.1

BioBlend versions 0.6.0 and 0.6.1 were released in June and July. BioBlend is a python library for interacting with CloudMan and the Galaxy API(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.) From the release CHANGELOG:

  • BioBlend.objects: Rename ObjDatasetClient abstract class to ObjDatasetContainerClient.

  • BioBlend.objects: Add ABCMeta metaclass and list() method to ObjClient.

  • BioBlend.objects: Add io_details and link_details parameters to ObjToolClient.get() method.

  • Open port 8800 when launching cloud instances for use by NodeJS proxy for Galaxy IPython Interactive Environments.
  • When launching cloud instances, propagate error messages back to the caller. The return types for methods create_cm_security_group, create_key_pair in CloudManLauncher class have changed as a result of this.

  • Add support for Python >= 3.3.

  • Add get_library_permissions() method to LibraryClient.

  • Add update_group(), get_group_users(), get_group_roles(), add_group_user(), add_group_role(), delete_group_user() and delete_group_role() methods to GroupsClient.

  • Add full_details parameter to JobsClient.show_job() (thanks to Rossano Atzeni).

  • BioBlend.objects: add ObjJobClient and Job wrapper (thanks to Rossano Atzeni).

  • BioBlend.objects: add check to verify that all tools in a workflow are installed on the Galaxy instance (thanks to Gianmauro Cuccuru).

  • Remove several deprecated parameters: see commits 19e168f and 442ae98.

  • Verify SSL certificates by default.
  • Add documentation about the Tool Sed and properly link all the docs on ReadTheDocs.

  • Solidify automated testing by using tox and flake8.

Planemo 0.13.0 through 0.13.2

https://pypi.python.org/pypi/planemo/

Planemo saw one major and several minor releases in the past two months. The most recent is v0.13.2. From the release history:

  • Fix for shed_init producing non-standard type hints. Issue 243, f0610d7

  • Fix tool linting for parameters that define an argument but not a name. Issue 245, aad1eed

  • Many doc updates including a tutorial for developing tools in a test-driven fashion and instructions for using the planemo appliance through Kitematic (with Kitematic screenshots from Eric Rasche).
  • If planemo cannot find a Galaxy root, it will now automatically fetch one (specifying --galaxy_install will still force a fetch). Pull Request 235

  • Documentation has been updated to reflect new and vastly improved Docker and Vagrant virtual appliances are now available, as well as a new VirtualBox OVA variant.

  • Update linting for new tool XML features (including detect_errors and output collections). Issue 233, 334f2d4

  • Fix shed_test help text. Issue 223

  • Fix code typo (thanks to Nicola Soranzo). Pull Request 230

  • Improvements to algorithm used to guess if an XML file is a tool XML file. Issue 231

  • Fix configuration file handling bug. Issue 240

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project.

Others

GalaxyProject
  • May 2015 Galaxy Release (v 15.05)

    Pulsar

    • Pulsar 0.5.0 was released in May. 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.

    CloudMan

    blend4j v0.1.2

    • blend4j v0.1.2 was released in December 2014. blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.


Other News


Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in June and July.