Freiburg News

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

We had to clear the queue due to an emergency today. We had noticed that a filesystem was extremely slow around 2 days ago, and had updated our Galaxy configuration to work around this. Unfortunately we failed to restart the handlers so new datasets continued to be written to that path, until the point at which it became an emergency and the system became completely unresponsive.

The European Galaxy Team is hiring!

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!

We all wish you a Merry Christmas and a Happy New Year. Enjoy the holiday season with your family and see you all next year. Our dear friend Martin Čech summed it up nicely :)

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

The 2019 Galaxy Community Conference (GCC2019) will be held in be held in Freiburg, Germany, 1-6 July. The training topics that are offered are determined by the community so BY YOU!

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.

ELIXIR France with the support of the ELIXIR Hub and the ELIXIR interoperability platform and in collaboration with COST CHARME, the National Bioscience Database Center (NBDC) and the Database Center for Life Science (DBCLS), organized last week (November 12th - 16th, 2018) a BioHackathon in Paris. Bérénice, Helena, Björn, and Saskia were there and represented the Galaxy Freiburg team and ERASMUS MC. The event was a total blast: 5 days in a remote area to work, code, have fun, eat and discuss with the 150 other participants from all Europe (even US)!

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.

We will be migrating Galaxy to new hardware. The hardware acting as the ‘head node’ is reaching End-of-Life and needs to be decomissioned.

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

We recently had the privilege of using the usegalaxy.eu’s new Training infrastructure as a Service (TIaaS) for our course on “Introduction to Galaxy and RNA-seq” at the Peter MacCallum Cancer Centre in Melbourne, Australia. Our own infrastructure was undergoing an upgrade and our planned workshop was going to be delayed but thanks to the TIaaS we were able to go ahead and run our workshop. All went smoothly and the feedback was very positive with 100% saying they would recommend the course to colleagues. A big thanks to the Galaxy EU team for providing this great resource.

“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.

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!, Yvan Le Bras, selects and presents a tutorial: “Galaxy 101”, from the topic “Introduction to Galaxy Analyses”

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

We have recently released a small utility we use for helping manage our Galaxy server. It is available on GitHub and includes many small SQL queries that administrators run every day.

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”.

A new Galaxy workshop on HTS data analysis was held in Freiburg last week.

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.

From 24th of June to 2nd of July the Galaxy Community Conference (GCC) and Bioinformatics Open Source Conference 2018 (BOSC) were meeting together in Portland, Oregon, United States. There was be two days of training, a two day meeting, and four days of intense collaboration. The meeting featured joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events. Bérénice, Joachim, and Björn were there and represented the Galaxy Freiburg team!

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

HiCExplorer - a tool suite for reproducible Hi-C data analysis, quality control and visualization was published a few days ago.

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.

Our database server crashed unexpectedly on friday night and we were down over most of the weekend.

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!

We had a temporary quota issue today when one of our developers working on automating UseGalaxy.eu Quota Increase Application made a mistake in the code which resulted in the legacy-users quota membership being removed.

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.

We’ve updated our Galaxy server to version 18.05. Additionally we have enabled the beta_gdpr_mode that the Freiburg Galaxy Team implemented in Galaxy.

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

The university’s home directory server went offline affecting numerous Galaxy jobs.

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 first Galaxy conference was held last week in Africa, organized by SANBI at University of Wester Cape in Cape Town. Björn and Bérénice participated:

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

More than 120 participants joined us for the first Galaxy User Conference in Freiburg. The first day has just ended and what an amazing day it was!

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 MiModD suite of tools, developed in the Baumeister lab at the Institute for Biology 3 here in Freiburg, is now available on the server. MiModD is for geneticists who have isolated phenotypic mutants of their favourite organism, e.g., through forward genetic screens, and who now wish to map the underlying mutations and eventually identify them molecularly.

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.

Our preliminary program for the Galaxy User Conference is now ready. You can fine more information here and register here.

We are part of COST Impact of Nuclear Domains On Gene Expression and Plant Traits

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!

Due to the high number of applicants for the next Galaxy workshop from 26.02.-02.03.2018, we close the registration. Participants will be selected from the applicants until 02.02.2018. The next workshop will take place in September 2018.

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.

New manuscript by Fidel Ramirez et al. about “High-resolution TADs reveal DNA sequences underlying genome organization in flies” was published today. Want to learn HiC data analysis? Try HiCExplorer in your tool menue!

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.

Tomas Klingström from the Swedish University of Agricultural Sciences and part of the amazing B3Africa project used the Freiburg Galaxy server for this training last week. Read his guest post here:

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.

Congrats to Stephan Nothjunge, Thomas Nührenberg, Ralf Gilsbach and many more from the Hein group for their new paper entiteled DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes.

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

Last wednesday we had a short, 1-hour maintenance period during which we upgraded the memory of the Galaxy head node. It was originally sitting at 32Gb of RAM but we ran into numerous issues handling the volume of jobs that are launched every day. We have since upgraded to 64Gb and performance has been smoother.

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

(from https://www.rz.uni-freiburg.de/rz/aktuell/vice-ws)

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

MultiQC is a tool that aggregate results from bioinformatics analyses across many samples into a single report. It is really a great and useful tool!

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

Our paper “Bioconda: A sustainable and comprehensive software distribution for the life sciences”, written with the great and big BioConda community, is now available as preprint on bioRXiv.

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

Our paper “Practical computational reproducibility in the life sciences”, written with Johannes Köster, Ryan Dale and several members of the US Galaxy team, is now available as preprint on bioRXiv.

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.

Björn was at the deNBI Summer School on Computational genomics and RNA biology organised by the RNA Bioinformatics center. He gave training on:

After 5 days, our HTS Galaxy workshop in Freiburg is over.

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

Many of you have noticed issues setting metadata recently. We had implemented a change with the hopes of fixing a bug we were seeing, however it had the unfortunate effect of causing most metadata setting jobs to fail.

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.

Björn and Bérénice were participating to ISBM/ECCB 2017 and particularly to Bioinformatics Open Source Conference (BOSC)) (satellite of ISBM/ECCB):

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.