Freiburg News

We’ve updated our Galaxy server to version 19.01.

A normal upgrade went awry and we had to restore some data from backup. We had a total downtime of around 20 hours.

Our admin Helena, in collaboration with the Rechenzentrum Uni Freiburg, has published “The Chimera and the Cyborg: Hybrid Compute: In vivo HPC, Cloud and Container Implementations”.

Find a summary of what is going on in the Galaxy community in March 2019.

Marina Veil, Lev Yampolsky and Daria Onichtchouk found that “Pou5f3, SoxB1, and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation”.

Johanna M. Walz et al. published about the “Impact of angiogenic activation and inhibition on miRNA profiles of human retinal endothelial cells”.

The Galaxy Community Conference starts with training but also continues with training throughout the conference. The community proposed some topics and now you need to vote to select the ones offered at GCC2019! Please take a few minutes to vote which ones should be offered at GCC2019! Thank you!

Dave B pointed us to this nice article about “Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform”.

This semester, the Faculty of Biology at the University of Belgrade offered for the first time an elective master course Introduction to Genomics which included several hands-on sessions on the Galaxy platform.

Last week, the Freiburg Galaxy team taught a 2 day course in the beautiful city of Belgrade!

The CernVM File System (CVMFS) provides a scalable, reliable and softare and data distribution service. It was originally developed to assist High Energy Physics (HEP) collaborations to deploy software on the worldwide-distributed computing infrastructure used to run data processing applications. The Galaxy project is using the same technology now to distribute 6TB of reference data and Singularity images to the scientific community. This will make analysis more reproducible across Galaxy instances as the reference data is also shared. However, the provided data can be used without Galaxy and for example will be available inside the de.NBI cloud.

Our next Galaxy Workshop on HTS data analysis from 25.2.-1.3.2019 in Freiburg is full. However, you can assign yourself to our waiting list.

Today we activated our brand new hardware. Thanks to the Federal Ministry of Education and Research we could extend the de.NBI-Cloud with 8x1TB nodes. This means more high-memory nodes for your memory intensive jobs, less waiting, faster results. Enjoy!

Maria Doyle has created a new tutorial about the visualization of RNA-Seq results with Volcano plots.

UseGalaxy.eu has now started automatically resubmitting any jobs which fail.

We’ve updated our Galaxy server to version 18.09. Everything went extremely smoothly.

Street Science community aims to make science tangible & accessible by bringing it to the “street” via open science workshops. In November, we had an unofficial kickoff of the BeerDEcoded project: we poured Beer into the MinION’s pores: sequencing yeast extracted from Beer with Nanopore.

European Galaxy Days were held 19 and 20 November 2018 in Freiburg, Germany. >40 participants from all Europe and even US meet for this two day gathering.

We have started to test a few of our workflows automatically against UseGalaxy.eu. This will run all workflows monthly to ensure that the keep working and that our infrastructure works and scales well.

The Galaxy community is developing and maintaining a collection of tutorials that are designed to be interactive and are built around Galaxy: https://training.galaxyproject.org. To help highlight our tutorials and the training effort of the community, a member of the community will select every month one tutorial and explains in the Galactic Blog why they select this tutorial. This month, the Galaxy contributor of the Month!, Saskia Hilteman, selects and presents a tutorial: “Reference-based RNA-Seq data analysis”, from the topic “Transcriptomics”

In a new manuscript Thomas Nührenberg et al. found that “Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome”.

Carolin Rommel et al. found that “The Transcription Factor ETV1 Induces Atrial Remodeling and Arrhythmia”.

“Selbst ist der Forscher: Big-Data-Analysen leicht gemacht”, a new German article written by The Freiburg Galaxy Team about our service and our work was published in the Laborpraxis.

Heinz is an algorithm for searching an optimal subnetwork from a bigger network. It can be applied to biological networks like gene regulation and protein-protein network to pinpoint the subnetwork of interest. We are pleased to announce that Heinz tools have been integrated into the Galaxy platform and are available on our server.

“Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis” by Achim Lother et al. was published in Journal of Endocrinology.

“Datenanalyse mit dem Galaxy Server”, a German article written by The Freiburg Galaxy Team about our service and our work was published in the Laborjournal.

The Galaxy community is developing and maintaining a collection of tutorials that are designed to be interactive and are built around Galaxy: https://training.galaxyproject.org. To help highlight our tutorials and the training effort of the community, a member of the community will select every month one tutorial and explains in the Galactic Blog why they select this tutorial. This month Maria Doyle has selected the tutorial “From peaks to genes”, from the topic “Introduction to Galaxy Analyses”.

The bwCloud which we relied on for cloud hosting has reach end of life, and is being replaced with bwCloud SCOPE. This documents our migration between the two clouds.

We had a confluence of unexpected and bad events which resulted in UseGalaxy.eu offline for a significant portion of yesterday (2018-09-20) afternoon. No data was lost.

The Freiburg Galaxy Team is looking for a JavaScript developer.

Users reported workflows were not running, we investigated and could not find the root cause but did solve the issue.

3 years ago the Galaxy community evaluated mechanism to make software installation more robust and we joined the Bioconda community, to fix the software deployment problem once and for all. Today, we are happy to annouce that the Bioconda manuscript is now published in the latest Nature Methods issue (public view). usegalaxy.eu and many other Galaxy instance are already powered by Bioconda and you might use it daily without knowing :)

Carolin Rommel, from the Institute of Experimental and Clinical Pharmacology and Toxicology, recently published her manuscript about “The Transcription Factor ETV1 Induces Atrial Remodeling and Arrhythmia”. Great work, congratulations Carolin!

We have leveraged the Galactic Radio Telescope to produce graphs of tool usage over time. You can embed these anywhere, in websites, in tool forms, etc.

Last week was CarpentryCon at University College Dublin, Ireland.

From 21st to 23rd of May was held a workshop for Galaxy training material and skills improvement at the Earlham Institut in Norwich. Bérénice and Björn were there!

Nanopolish is a popular tool suite for working with data produced by the Nanopore sequencing platform. We are pleased to announce that the demanding tools have been integrated into the Galaxy platform and are available on our server.

The Galaxy project has published an 2018 update of the core Galaxy framwork with all the new features of the last two years. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

It’s with incredible sadness that we need to notify you that Christophe Caron passed away. He suffered a heart attack during a football game last Friday.

Google’s DNS stopped responding to requests for usegalaxy.eu for 35 minutes.

The Galaxy Team in Freiburg has a new member.

The registration for our next Galaxy Workshop on HTS data analysis from 17-21 September 2018 in Freiburg is open. We have 30 places. More information can be found in events on our homepage. Participants are selected from the applicants. Apply now!

The Galaxy User Conference in Freiburg just ended!

As part of our ongoing growth and development, Freiburg Galaxy is becoming useGalaxy.eu

The ELIXIR Galaxy community kick-off meeting was held here in Freiburg.

We have written a utility to help you propagate tags through your histories. Did you forget to tag the inputs before running a long workflow? We’ve now solved this issue.

The deepTools developers have released a brand new version! This time with CRAM support, new normalization and plotting options, new tools, e.g. alignmentsieve for ATAC-seq, and many more.

We are happy to announce that we are hosting the ELIXIR Galaxy community kick-off meeting here in Freiburg. ELIXIR members meet at 14.03.2018 starting from 13:00 at the technical faculty of the University of Freiburg. Everyone is invited to join, but please let us know so that we can plan accordingly. More information you can found here.

During the last month the Galaxy team has put a lot of effort into updating the Genome Annotation tools and has included new tools that will change how you work with your Genome in silico.

Congratulation to Ralf Gilsbach et al. from the Hein group for their great new paper entiteled Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo.

Because many people already asked: The autumn Galaxy Workshop on high-throughput data analysis will take place from 17.-21.9.2018 here in Freiburg. Registration will be open from mid of April 2018 on. Save the date!

The Freiburg Galaxy Team is looking for 2 Postdoctoral researchers.

New generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.

“Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes” by Kerstin Thriene et al. was published today in Molecular and Cellular Proteomics. Thanks to Kerstin, Jörn and Collegues for this great collaboration.

We had a very nice Galaxy Admin workshop in Oslo.

Today (2017-12-11) we had a temporary outage of job executions. We’ve been making progress on a new job configuration system for our Galaxy which should let us reconfigure job scheduling in a more dynamic way. After weeks of work and testing we’re finally rolling this out to 6% of our users. Unfortunately as part of the deployment we failed to install two dependencies that were required as part of the new changes.

Our paper “Community-driven data analysis training for biology” about the Training material we are developing with the Galaxy Training Network is now available as preprint on bioRXiv.

Congrats to Douglas M. Lopes, et. al from the Franziska Denk group at King’s College London for their new paper Sex differences in peripheral not central immune responses to paininducing injury.

Yesterday (2017-11-20) all upload jobs and some other tools were failing to be launched on our cluster. One of our clusters became unresponsive and the code which handled job distribution to clusters had to be updated. This process required three iterations to get correct. Each update cycle took ~15-20 minutes due to our update process and how long it takes Galaxy to switch over to the new configuration.

We are offering another Galaxy workshop on HTS data analysis. Please apply here.

We just updated our Galaxy server to version 17.09! Actually this was done by H. Rasche, our new team member! Welcome Helena!

We updated our tools stack - more than 90 tools were updated to newest versions!

Do you have Nanopaore or PacBio reads? Try minimap2 as a new aligner! From minimaps homepage:

Thanks to a contribution from Melanie Föll (Schilling Lab) we have added tools for analysing imaging mass spectrometry data.

Joachim presented the developments of HiCExplorer at the 5th early-stage researchers Next-Generation Sequencing Symposium in Heidelberg.

During the de.NBI Symposium 2017, Bérénice presented the poster “Building an open, collaborative, online infrastructure for bioinformatics training”.

Bérénice was helping Toby Hodges, Malvika Sharan and the other instructors for the Software Carpentry workshop organized at EMBL in Heidelberg.

Björn participated to the Wellcome Trust funded MetaboFlow meeting (training and hackathon) in Birmingham.

Björn, Yasset Perez-Riverol (EBI), and the French ELIXIR node organised a BioContainer Hackathon in Paris.

We have been experimentally running some Galaxy jobs in the bwCloud at the University of Freiburg. Unlike more traditional compute resources we can scale the cloud resources up and down on-demand.

A subset of upload jobs were hanging. Investigation pointed to a handful of VMs that were recently launched in our cloud which were firewalled off from access. Condor, our job scheduler, needs to be able to reach the VMs in order to send jobs to it. When jobs were scheduled for those VMs, they just hung indefinitely. We have now corrected the issue in code, so we won’t launch any more VMs with this issue.

Maϊwen Caudron-Herger and Sven Diederichs published about “Mitochondrial mutations in human cancer: Curation of translation”.

During the German Conference on Bioinformatics in Tübingen, we presented (with Milad Miladi) 3 posters related to Galaxy:

Today our Galaxy server has calculated its 2.000.000th job! Thanks to all our users and people that have contributed to this project!

We added to the instance ENASearch, a tool for interacting with ENA’s API. It allows you to search and retrieve data from ENA directly inside Galaxy.

For the mapping of non-contiguous transcripts, this program was developed. STAR’s speed and reliability have been proven. The mapper was recently updated on this server and several often used reference genomes are already online.

Our friends from Workflows4Metabolomics have updated there tools and workflows to version 3.0 - and so did we. Enjoy all the great new tools dedicated to metabolomics data processing, analysis and annotation for Metabolomics community.

Clemens, Björn and Bérénice were participating in the Galaxy Community Conference GCC training: