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GalaxyUpdates/2014_11

November 2014 Galaxy Update

Galaxy Updates

Welcome to the November 2014 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.

Thanks!

Thanks to everyone who took the Galaxy Questionnaires in October. We received 155 responses, which is an amazing number. We will use this input to help prepare the next grant for the Galaxy Project. Thanks again for your time and thoughtful responses.

IRC Channel is Now Publicly Archived

Galaxy IRC Channel archive at BotBot

The #galaxyproject IRC channel now has an online public archive. These archives have also been included in the Galaxy search engines. The archive started on October 22, 2014.

This was proposed and then discussed, and approved on Galaxy Biostar.

Galaxy Training Network

Galaxy Training Network

The Galaxy Training Network (GTN) was launched October 16 with 16 charter member organizations. The GTN is a network of trainers who teach bioinformatics using Galaxy, or teach about Galaxy itself. The GTN aims to make it easy to find Galaxy trainers, and to share and discover the wealth of training resources available for Galaxy. This includes training materials, a trainer directory, best practices, and guidance on computing platforms for teaching with Galaxy. The Galaxy Training Network is accessible to the entire community.

If you teach with Galaxy, then please consider adding your organization, materials, and best practices. Since the GTN launched two weeks ago, 4 new organizations have joined:

This brings the total to 20 training organizations on 5 continents.

Events

Galaxy Days: 2-3 December, Paris

The French Working Group GALAXY-IFB (Institut Français de Bioinformatique) is organizing a second session around the Galaxy portal. The event will be at Institut Curie in Paris over two days. This year, we want to involve two communities: biologists (also known as Galaxy 'users') and bioinformaticians (Galaxy 'developers'). The goal is to present user experience around the portal, from a single user to a wider community:

  • Dec 2 (13:30-17:30): Galaxy's user experiences, and discussion on how the platform is (or is not) useful for building analysis.
  • Dec 3 (09:00-17:00): Technology talks (new environment, Galaxy in production, ...)

Interested? Please contact <ifb DOT galaxy AT sb DASH roscoff DOT fr> for more information.

The French IFB Galaxy Working Group:

URGI, GenoToul, MIGALE, PFEM, SouthGreen, Institut Curie, ABiMS

URGI   GenoToul   MIGALE   PFEM   SouthGreen Institut Curie   ABiMS

Swiss German Galaxy Tour 2014 Report

Swiss-German Galaxy Tour 2014

After the big success of the first Swiss Galaxy Workshop two years ago, we decided to organize a similar event again this fall. This time, we added a training day prior to the workshop, and a developer day after the workshop. The first two days were held in Bern (Switzerland), and the third in Freiburg (Germany). Hence we called the whole event: "Swiss German Galaxy Tour 2014".

More than 40 people registered for the event, signing up for one, two or all three days, ...
- read more -

Fall 2014 GUGGO Events Report

Galaxy User Group Grand Ouest (GUGGO)

Three events were sponsored by the Galaxy User Group Grand Ouest (GUGGO) in western France earlier this fall. Summaries of all 3 events are now available online.

The Tools integration on Galaxy Workshop was held 11 September. The summary includes ...
- read more -

Other Events

Des bonnes pratiques d'intégration d'outils sous Galaxy   Galaxy Training Days   Analisi dati Next Generation Sequencing in Galaxy   Workshop: Extended RNA-Seq analysis RNA-Seq & ChIP-Seq analysis course using Galaxy

http://bit.ly/gxycal

There are upcoming events in France, Germany, Australia, Italy, and the United States. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date

Topic/Event

Venue/Location

Contact

November 3-5

Des bonnes pratiques d'intégration d'outils sous Galaxy

Workshop full, but you can get on the waiting list

Station Biologique de Roscoff, France

Christophe Caron <christophe.caron@sb-roscoff.fr>

November 3-5

Galaxy NGS Training in the Group of Prof. Dr. Bettina Kempkes

Workshop full, but you can get on the waiting list

Helmholtz Zentrum München, Germany

Björn Grüning <bjoern.gruening@gmail.com>

November 3-6

Galaxy training days

Workshop full, but you can get on the waiting list

INRA de Toulouse Midi-Pyrénées, France

GenoToul Bioinformatics Team

November 5-8

Rapidly bringing software to biologists with Galaxy and Docker

Biological Data Science, Cold Spring Harbor Laboratory, New York, United States

John Chilton

Building Galaxy Japan community

Ryota Yamanaka

November 16

Deciphering Big Data Stacks: An Overview of Big Data Tools

Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC-14), Supercomputing 2014 (SC14), New Orleans, Louisiana, United States

Enis Afgan

November 18-20

Analisi dati Next Generation Sequencing con Galaxy

Cagliari, Italy

CRS4 <ngs-courses@crs4.it>

November 19-20

Workshop: Extended RNA-Seq analysis

The University of Queensland, Brisbane, Queensland, Australia

Mark Crowe

November 21

Galaxy Cluster to Cloud - Genomics at Scale

GCE: The 9th Gateway Computing Environments Workshop, Supercomputing 2014 (SC14), New Orleans, Louisiana, United States

Enis Afgan

November 26-28

RNA-Seq & ChIP-Seq analysis course using Galaxy

PRABI, Lyon, France

Navratil V <navratil AT prabi DOT fr>., Oger C. <oger AT prabi DOT fr>, Veber P. <veber AT prabi DOT fr>, Deschamps C. <deschamps AT prabi DOT fr>, Perriere G. <perriere AT prabi DOT fr>

December 2-3

Galaxy Day

Institut Curie, Paris, France

IFB Galaxy <ifb DOT galaxy AT sb DASH roscoff DOT fr>

December 5-8

Next Generation Data Analysis Workshop

UC Riverside, Riverside, California, United States

Rakesh Kaundal <rkaundal AT ucr DOT edu>

December 9-11

Microarray data analysis on Galaxy

BIRD IFB core facility Nantes University/INSERM, Nantes, France

Raluca Teusan <raluca DOT teusan AT inserm DOT fr>, Audrey Bihouée, Edouard Hirchaud

December 16-19

RNA-Seq and ChIP-Seq Analysis with Galaxy

UC Davis, California, United States

UC Davis Bioinformatics Training <bioinformatics DOT core AT ucdavis DOT edu>

2015

January 10-14

Galaxy for SNP and Variant Data Analysis

Plant and Animal Genome XXIII (PAG2014), San Diego, California, United States

Dave Clements

February 9-13

Analyse bioinformatique de séquences sous Galaxy

Montpellier, France

J.F. Dufayard <jean-francois.dufayard@cirad.fr>

February 16-18

Managing and Disseminating Tools and Data in Galaxy

Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States

James Taylor

July 6-8

2015 Galaxy Community Conference (GCC2015)

The Sainsbury Lab, Norwich, United Kingdom

Galaxy Outreach <outreach@galaxyproject.org>

New Papers

38 papers were added to the Galaxy CiteULike Group in October, including:

The new papers were tagged in these areas:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

4

Cloud

-

Project

4

Tools

3

UsePublic

-

HowTo

3

RefPublic

-

UseCloud

-

Visualization

3

IsGalaxy

1

Reproducibility

2

UseLocal

8

Workbench

19

Methods

4

Shared

6

UseMain

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.


New Public Servers

Two new public Galaxy servers were added to the published list in October:

Majewski Lab Galaxy

Majewski Lab: ExomeAI

The Majewski Lab ExomeAI Server supports detection of recurrent allelic imbalance in tumors using whole exome sequencing data, using ExomeAI, a free web-based application for detection of recurrent AI/LOH segments in tumor samples. Support is provided in the ExomeAI Manual, and via email <Javad DOT Nadaf AT gmail DOT com>. See Nadaf J, Majewski J, Fahiminiya S. (2014). ExomeAI: Detection of recurrent Allelic Imbalance in tumors using whole Exome sequencing data. Bioinformatics. 2014 Oct 8.

The Majewski Lab ExomeAI Server is supported by the McGill University and Génome Québec Innovation Centre

OSDD Molecular Property Diagnostic Suite (MPDS)

Molecular Property Diagnostic Suite (MPDS)

The OSDD Molecular Property Diagnostic Suite (MPDS) Galaxy servers is an OSDD Chemoinformatics Portal. MPDS exposes a software toolset that rationally diagnoses (druggable) molecules. MPDS 1.0 consists of six modules covering informatics (DataBases, File format conversion), structure and analogue based drug design approaches (Property calculation, QSAR, Docking). Support is available.

MPDS is developed under the broad initiative of OSDD (Open Source Drug Discovery) of CSIR (Council of Scientific and Industrial Research, Govt. of India). The site is being hosted from IICT, Hyderabad, India.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   
Describe your instance now



There were no new Log Board or Deployment Catalog entries in August! 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.


Galaxy ToolShed

New Releases

BioBlend v0.5.2 was released in October. BioBlend is a python library for interacting with CloudMan and the Galaxy API.

New versions of Galaxy, CloudMan, and blend4j were all released in August.

Look for a new Galaxy distribution in November.

ToolShed Contributions

Galaxy Project ToolShed Repos

Here are new contributions for the past two months.

In no particular order:

Tools

  • From crs4:

  • From arkarachai-fungtammasan:

    • microsatellite_ngs: Pipeline to profile and genotype microsatellites from short read data. This repository contains these sets of tools: 1 create microsatellite length profile, 2 correct for sequencing errors and report genotype, 3 estimate minimum sequencing read depth, 4 convert informative read depth to locus specific/genome wide sequencing depth.

  • From peterjc:

    • mummer: v0.0.1, essentially a preview (previously only on the TestToolShed). A simple wrapper allowing MUMmer to be used to draw dotplots from within Galaxy using mummer, mucmer, or promer with mummerplot. No tests yet, no gnuplot or ps2pdf dependency yet.

  • From devteam:

    • picard_plus: Picard wrappers for version 122 and up. New set of Picard wrappers that do not rely on external scripts and deal with all aspects of picard management and UI via tool XML.

  • From saket-choudhary:

  • From galaxyp:

Workflows

Packages / Tool Dependency Definitions

  • From takadonet:

    • package_tbl2asn_23_7: Contains a tool dependency definition that downloads the binary version 23.7 of tbl2asn. tbl2asn is an automated bulk submission program.

    • package_minced_0_1_6: Contains a tool dependency definition that downloads version 0.1.6 of minced, a CRISPR finder. MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the command-line and was derived from CRT (http://www.room220.com/crt/): Charles Bland et al., CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics 8, no. 1 (2007): 209.

    • package_barrnap_0_5: Contains a tool dependency definition that downloads and compiles version 0.4 of the barrnap. Barrnap predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequ It takes FASTA DNA sequence as input, and write GFF3 as output. https://github.com/Victorian-Bioinformatics-Consortium/barrnap

  • From iuc:

    • package_numpy_1_9: Contains a tool dependency definition that downloads and compiles version 1.9 of the the python numpy package. NumPy is the fundamental package for scientific computing with Python.

    • package_blast_plus_2_2_30: first version, based on BLAST+ 2.2.29 definition. NCBI BLAST+ 2.2.30 (binaries only) This Tool Shed package is intended to be used as a dependency of the Galaxy wrappers for NCBI BLAST+ and any other tools which call the BLAST+ binaries internally.

    • package_matplotlib_1_4: Contains a tool dependency definition that downloads and compiles version 1.4.x of the the python matplotlib package. matplotlib is a python 2D plotting library which produces publication quality figures. This is the version 1.2.x of matplotlib. www.matplotlib.org/

    • package_networkx_1_9: Contains a tool dependency definition that downloads and compiles version 1.9.x of the python library networkx. NetworkX is a Python language software package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. http://networkx.github.io/

    • package_scipy_0_14: Contains a tool dependency definition that downloads and compiles version 0.14 of the the scipy python library. SciPy is open-source software for mathematics, science, and engineering. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. http://www.scipy.org/

    • package_dill_0_2: Contains a tool dependency definition that downloads and compiles version 1.9.x of the python library dill. Dill extends python's 'pickle' module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. http://trac.mystic.cacr.caltech.edu/project/pathos/wiki/dill

    • package_scikit_learn_0_15: Contains a tool dependency definition that downloads and compiles version 0.15.x of the the scikit-learn package. Easy-to-use and general-purpose machine learning in Python. Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. http://scikit-learn.org/

  • From saket-choudhary:

  • From lparsons:

    • package_cutadapt_1_6: Initial version Contains a tool dependency definition that downloads and compiles cutadapt version 1.6 trim adapters from high-throughput sequencing reads

  • From devteam:

Workflows

Select Updates

  • From lparsons:

  • From saskia-hiltemann:

    • ireport: fixed dependencies and added MarkDown support

  • From devteam:

  • From crs4:

    • sspace: Update Orione citation. Update dependency to SSPACE Basic v2.1 . Add <citations>.

    • prokka: Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.

  • From devteam:

  • From miller-lab:

Other News