May 2019 Galactic News

GCC2019 registration / Poster/Demo abstracts / sponsors, GTN CoFest, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more!

May 6th 2019

Galaxy News

The May 2019 Galactic News is here! This is a summary of what is going on in the Galaxy community.

If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.


GCC2019 Registration

Registration for the 2019 Galaxy Community Conference (GCC2019) is open! Discounted registration rates are available until 17MAY19.

GCC2019

GCC2019 will be held 1-6 July in Freiburg, Germany. The tenth GCC will have many familiar features from earlier years, including accepted and lightning talks, posters and demos, birds-of-a-feather gatherings (BoFs), training, and a CollaborationFest. GCC2019 brings the most significant conference program update in several years:

  • some training will be integrated with the main conference,
  • three days of conference instead of two,
  • several parallel sessions,
  • and a strong emphasis on organizing content by domain.

GCC2019, like every GCC before it, will be built around community. Training topics are nominated, selected, and presented by the community. Presentations will feature the full spectrum of Galaxy applications, enhancements and deployments from the community as well.

If you are working in data intensive life science research then there will not be a better place to share your work, learn from others, and find new collaborators.

Please find additional information on GCC2019 here.

Poster & Demo Abstract Submission is Still Open

The talk submission abstract deadline was last week, but poster and demo submissions remain open! Got something to show? Submit an abstract.

Fellowships: 2nd Round Due this Friday

Travel fellowships to attend GCC2019 are available. If you are interested, apply by this Friday, 10 May.

Sponsors

We are delighted to have GigaScience as a returning sponsor:

GigaScience

GigaScience Journal

GigaScience is an online open access, open data, open peer-review journal published by Oxford University Press and BGI. The journal offers ‘big data’ research from the life and biomedical sciences, and on top of 'Omics research includes the growing range of work that uses difficult-to-access large-scale data, such as imaging, neuroscience, ecology, systems biology, and other new types of shareable data. GigaScience is unique in the publishing industry as it publishes all research objects (data, software tools, source code, workflows, containers and other elements related to the work underpinning the findings in the article). Promoting Open Science, all published software needs to be under an OSI-license, all supporting data must be available and open, and all peer review is carried out transparently. Presenting workflows via our GigaGalaxy.net server, novel work presented at the meeting utilising Galaxy is eligible to a 15% APC if it is submitted to our Galaxy series.

GTN CoFest and community call

The Galaxy Training Network has developed an infrastructure to deliver interactive training based on Galaxy: one central place to aggregate training materials covering many current research topics. Each topic is supported by different tutorials developed and maintained by the community via a GitHub repository.

GTN cofest logo

The Galaxy Training Network is organizing regular online CoFests (Collaboration/Contribution Fests) every 3 months on the 3rd Thursday for a day of the collaborative work on the training content.

The next one will be on the 16th of May. Anyone who would like to contribute on any other topics is very welcome to join.

We will coordinate via Hangout (drop-in channel we will keep open the whole day) and the GTN Gitter channel.

During the day, we plan to have GTN community calls to discuss the recent changes and future directions. To accommodate different time zones and schedules, we will have 2 calls (with similar discussions) at 8am (UTC + 2) and 4pm (UTC + 2) via Hangout.

If you want to join to help or to talk and learn about the project, let us know on the Gitter channel or by leaving a comment on the issue on GitHub

Upcoming events

These and other Galaxy related events are coming up:

Date Topic/Event Venue/Location Contact
May 7th 2019 Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space (AnVIL) Biology of Genomes, CSHL, Cold Spring Harbor, New York, United States James Taylor
May 13th 2019 Initiation à l’utilisation de Galaxy Cycle "Bioinformatique par la pratique" 2019, INRA, Jouy-en-Josas, France Training offered by GTN MemberVéronique Martin
May 13th 2019 Science Gateways Bootcamp Indianapolis, Indiana, United States help@sciencegateways.org.
May 14th 2019 Analyse avancée de séquences Bordeaux, France Training offered by GTN MemberMacha Nikolski
May 14th 2019 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy Cycle "Bioinformatique par la pratique" 2019, INRA, Jouy-en-Josas, France Training offered by GTN MemberVéronique Martin
May 16th 2019 GTN CoFest and community call Online Bérénice Batut, Saskia Hiltemann
May 17th 2019 Initiation aux analyses de données transcriptomiques IRD, Montpellier, France Training offered by GTN MemberFormateurs
May 23rd 2019 Initiation aux analyses de données metabarcoding IRD, Montpellier, France Training offered by GTN MemberFormateurs
June 2nd 2019 Galaxy @ ASMS 2019 ASMS 2019, Atlanta, Georgia, United States Tim Griffin, Pratik Jagtap
June 11th 2019 Bioinformatics for Beginners National Institutes of Health (NIH), Bethesda, Maryland, United States training@faes.org
June 12th 2019 Traitement bioinformatique et analyse différentielle de données d'expression RNA-seq sous Galaxy Cycle "Bioinformatique par la pratique" 2019, INRA, Jouy-en-Josas, France Training offered by GTN MemberVéronique Martin
July 1st 2019 2019 Galaxy Community Conference (GCC2019) Freiburg, Germany Training offered by GTN MemberOrganizers
July 3rd 2019 An introduction to Galaxy with the NeCTAR Genomics Virtual Laboratory 2019 Winter School in Mathematical & Computational Biology, Brisbane, Queensland, Australia Training offered by GTN MemberIgor Makunin
July 29th 2019 Getting started with Galaxy and NGS Platforms QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
July 30th 2019 Genome assembly using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
July 31st 2019 Variant detection using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
August 1st 2019 RNA Seq analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
August 1st 2019 "Teaching undergraduate genomics with Galaxy” and “Resources and recommendations for teaching undergraduate genomics with Galaxy" ASMCUE 2019, Tyson, Virginia, United States Training offered by GTN MemberMohammad Heydarian, Anton Nekrutenko
August 2nd 2019 Metagenomics analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org

Publications

265 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in the last month, pushing the total number of pubs past 7500.

Highlighted Publications

There were 15 Galactic and Stellar publications added. Here are the open access ones.

Publication Topics

# Tag # Tag # Tag # Tag
162 +Methods 66 +UsePublic 36 +Workbench 26 +RefPublic
19 +UseMain 18 +Reproducibility 13 +UseLocal 9 +IsGalaxy
8 +Cloud 6 +Shared 5 +HowTo 5 +Tools
4 +Other 2 +Education 1 +Unknown

Galaxy Platforms News

The Galaxy Platform Directory lists resources for easily running your analysis on Galaxy, including publicly available servers, cloud services, and containers and VMs that run Galaxy. A lot was added in March:

Single Cell Omics Galaxy workbench

scworkbench

The Single Cell Omics workbench is a comprehensive set of analysis tools and consolidated workflows for single cell analysis. The current implementation comprises more than 20 bioinformatics tools dedicated to different research areas of single cell biology.

NetworkAnalyst

networkanalyst

NetworkAnalyst is an online analysis environment for transcriptome profiling, network analysis, and meta analysis for gene expression data. NetworkAnalyst has developed and made available a public Galaxy server to support raw RNAseq processing for 17 species covering mammals, birds, bacteria, plants and parasites.

CellOrganizer

cellorg

CellOrganizer creates generative models of the spatial organization of cells from microscope images and automatically provides geometries for spatial simulations of cell processes and behaviors. A Galaxy server provides access to CellOrganizer tools for users who do not have the resources to run the Matlab or Docker versions.

CIRM-CFBP

cirmcfbp

International Center for Microbial Resources - Plant Associated Bacteria (CIRM-CFBP) is providing web based access to tools (SkIf and KI-S) of IRHS-EmerSys lab on the CIRM-CFBP Galaxy instance.

gcac

Galaxy for Compound Activity Classification

Galaxy for Compound Activity Classification (GCAC)is a one stop solution for data generation, data preparation, feature selection, model building, prediction and retrieval of potential molecules. GCAC is available as a public Galaxy server, a VM, and an installable Galaxy tool suite from the toolshed.

MGS-FAST

mgsfast

MGS-Fast is an analysis approach to rapidly map a metagenomics shotgun sequencing (MGS) data set and assign known functions to reads originating from microbial genes, producing counts of KEGG gene orthologs as output. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.

Galaxy Platforms in Publications

We tag papers that use, mention, implement or extend public Galaxy platforms (servers, services, clouds, containers...). Here are the platforms that were referenced at least twice in the past month's publications:

# Tag # Tag # Tag # Tag
19 >Huttenhower 11 >ARGs-OAP 9 >RepeatExplorer 7 >Workflow4Metabolomics
5 >Galaxy-P 4 >Orione 4 >UseGalaxy.eu 4 >UseGalaxy.org.au
3 >epiGeEC 2 >APOSTL 2 >ARGalaxy 2 >CIRM-CFBP
2 >deepTools 2 >Pasteur 2 >SymD

ggcp

New Galactic Blog Post

This month we have a Galactic Blog post where Enis Afgan and Vahid Jalili describe recent efforts to Build up support for the Google Cloud Platform in Galaxy.


Who's Hiring

Please Help! Yes you!

The dark energy of irreproducible research is threatening the science universe! Please help the Galaxy push it back!

Have 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.


Doc, Hub, and Training Updates

Updates from the Galaxy Training Materials in April:

Hub

The User Authentication and Authorization docs explain all of Galaxy's features that (a) enable users to login to Galaxy using their social and institutional identities (e.g., using their Google account), and (b) allows them to securely authorize Galaxy to access their private cloud-based resources. Both (a) and (b) are described for admins (how to configure Galaxy for that feature) and users (how to use that feature) separately. Many thanks to Vahid Jalili, Kjell Petersen, and Enis Afgan for their contributions.

Also see Vahid Jalili's slides on User Authentication and Cloud Authorization in the Galaxy project

GTN Training Materials

Galaxy Training Materials


ToolShed Contributions

Galaxy ToolShed

We didn't get to this this month. Look forward to a double dose of tools next month.

Releases

New additions to the Galaxy Ecosystem.

Galaxy-parsec 1.12.1

Parsec is a set of automatically generated wrappers for BioBlend functions. I found myself writing a large number of small / one-off scripts that invoked simple bioblend functions. These scripts were impossible to compose and use in a linux-friendly manner. I copied and pasted code between all of these utility scripts.

Parsec is the answer to all of these problems. It extracts all of the individual functions I was writing as separate CLI commands that can be piped together, run in parallel, etc.

Pulsar 0.9.1

Pulsar

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.

galaxy-lib 19.5.2

galaxy-lib is a subset of the Galaxy core code base designed to be used as a library. This subset has minimal dependencies and should be Python 3 compatible. It's available from GitHub and PyPi.


Other News