UseGalaxy.eu update to 19.01March 19, 2019 Freiburg release
We’ve updated our Galaxy server to version 19.01.
UseGalaxy.eu Downtime on 18th MarchMarch 18, 2019 Freiburg devops downtime
A normal upgrade went awry and we had to restore some data from backup. We had a total downtime of around 20 hours.
New Paper - Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)March 15, 2019 Freiburg paper
In collaboration with our cooperation partner at the Scientific Computing Research Unit, University of Cape Town, we have recently published “Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)”. This publication provides a basis for performing molecular dynamics simulations and analysis through Galaxy, using a number of commonly used packages, such as NAMD, GROMACS and CHARMM (for simulation) and Bio3D and MDAnalysis (for analysis).
New Paper The Chimera and the CyborgMarch 14, 2019 Freiburg paper
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”.
Galactic NewsMarch 5, 2019 Freiburg galaxy
Find a summary of what is going on in the Galaxy community in March 2019.
A(nother) successful Galaxy HTS data analysis workshop in FreiburgMarch 4, 2019 Freiburg training
Last week, the Freiburg Galaxy team taught a 5 day workshop on HTS data analysis in Freiburg!
New Paper on "Pou5f3, SoxB1, and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation."February 11, 2019 Freiburg paper
Marina Veil, Lev Yampolsky and Daria Onichtchouk found that “Pou5f3, SoxB1, and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation”.
New Paper on "Impact of angiogenic activation and inhibition on miRNA profiles of human retinal endothelial cells."February 11, 2019 Freiburg paper
Johanna M. Walz et al. published about the “Impact of angiogenic activation and inhibition on miRNA profiles of human retinal endothelial cells”.
Tool Quest: Do you know the answer?February 9, 2019 Freiburg training
Last week we got a request from on of our users with a tricky question:
Vote for the Training during the next Galaxy Community ConferenceJanuary 27, 2019 Freiburg training
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!
The GOEnrichment tool and tutorial are now available on Galaxy, by Daniel SobralJanuary 25, 2019 Freiburg release
Galaxy enhances Introduction to Genomics as part of Master program in Belgrade, by Nevena VeljkovicJanuary 25, 2019 Freiburg training
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.
A successful Galaxy RNA-seq workshop in BelgradeJanuary 19, 2019 Freiburg training
Last week, the Freiburg Galaxy team taught a 2 day course in the beautiful city of Belgrade!
Queue clearedJanuary 18, 2019 Freiburg devops downtime
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.
Another European CVMFS mirror is onlineJanuary 11, 2019 Freiburg devops
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.
New hardware: 8x1TB memory nodesJanuary 8, 2019 Freiburg devops release
New tutorial: Visualization of RNA-Seq results with Volcano PlotDecember 31, 2018 Freiburg tutorial
Maria Doyle has created a new tutorial about the visualization of RNA-Seq results with Volcano plots.
Gajan Kristnaskon kaj bonan novjaron!December 25, 2018 Freiburg devops
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 :)
Automatic resubmission of failed Galaxy jobsDecember 19, 2018 Freiburg devops
UseGalaxy.eu has now started automatically resubmitting any jobs which fail.
UseGalaxy.eu update to 18.09December 11, 2018 Freiburg release
We’ve updated our Galaxy server to version 18.09. Everything went extremely smoothly.
Nominate a training for the 2019 Galaxy Community Conference (GCC2019)December 3, 2018 Freiburg training
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!
BeerDEcoded: unofficial kickoffNovember 30, 2018 Freiburg training
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 Biohackathon in ParisNovember 23, 2018 Freiburg training
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)!
Tutorial of the Month: "Reference-based RNA-Seq data analysis", selected by Saskia HiltemannNovember 15, 2018 Freiburg training
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”
Upcoming Server MigrationNovember 7, 2018 Freiburg devops
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.
New Paper on "Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome"November 5, 2018 Freiburg paper
In a new manuscript Thomas Nührenberg et al. found that “Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome”.
New Paper on "The Transcription Factor ETV1 Induces Atrial Remodeling and Arrhythmia."November 2, 2018 Freiburg paper
Carolin Rommel et al. found that “The Transcription Factor ETV1 Induces Atrial Remodeling and Arrhythmia”.
Training Infrastructure Feedback from Maria DoyleOctober 31, 2018 Freiburg training tiaas
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.
New article 'Selbst ist der Forscher: Big-Data-Analysen leicht gemacht'October 30, 2018 Freiburg paper
“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 tools for network analysis over transcriptomics datasetsOctober 17, 2018 Freiburg tools training
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.
Tutorial of the Month: "Galaxy 101", selected by Yvan Le BrasOctober 15, 2018 Freiburg training
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”
New Paper on "Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis"October 10, 2018 Freiburg paper
“Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis” by Achim Lother et al. was published in Journal of Endocrinology.
Tutorial of the Month: Maria Doyle selected "From peaks to genes"October 2, 2018 Freiburg training
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”.
Cloud Migration PostmortemSeptember 26, 2018 Freiburg devops downtime
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.
A successuful Galaxy HTS data analysis workshopSeptember 24, 2018 Freiburg training
A new Galaxy workshop on HTS data analysis was held in Freiburg last week.
UseGalaxy.eu DowntimeSeptember 21, 2018 Freiburg devops downtime
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.
Freiburg Galaxy Team has an open position!July 25, 2018 Freiburg job
GCCBOSCJuly 18, 2018 Freiburg training
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!
Temporarily Held Workflow InvocationsJuly 12, 2018 Freiburg devops downtime
Users reported workflows were not running, we investigated and could not find the root cause but did solve the issue.
Bioconda: sustainable and comprehensive software distribution for the life sciencesJuly 4, 2018 Freiburg paper
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 :)
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualizationJuly 4, 2018 Freiburg paper
HiCExplorer - a tool suite for reproducible Hi-C data analysis, quality control and visualization was published a few days ago.
The Transcription Factor ETV1 Induces Atrial Remodeling and Arrhythmia.July 3, 2018 Freiburg paper
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!
Database outage affecting UseGalaxy.euJune 18, 2018 Freiburg devops downtime
Our database server crashed unexpectedly on friday night and we were down over most of the weekend.
Workshop for Galaxy training material and skills improvementJune 5, 2018 Freiburg training
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 tools for signal-level analysis of Oxford Nanopore sequencing data is now available in GalaxyMay 30, 2018 Freiburg tools
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 updateMay 28, 2018 Freiburg paper
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.
UseGalaxy.eu update to 18.05 and GDPRMay 25, 2018 Freiburg release
We’ve updated our Galaxy server to version 18.05. Additionally we have enabled
beta_gdpr_mode that the Freiburg Galaxy Team implemented in Galaxy.
In memory of Christophe CaronMay 7, 2018 Freiburg
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.
DNS outage affecting UseGalaxy.euApril 26, 2018 Freiburg devops downtime
Google’s DNS stopped responding to requests for usegalaxy.eu for 35 minutes.
Fileserver Outage affecting JobsApril 24, 2018 Freiburg devops downtime
The university’s home directory server went offline affecting numerous Galaxy jobs.
New Galaxy Team member!April 23, 2018 Freiburg galaxyteam
The Galaxy Team in Freiburg has a new member.
Galaxy Workshop registration open!April 18, 2018 Freiburg training
Galaxy User Conference: second and last dayMarch 16, 2018 Freiburg
The Galaxy User Conference in Freiburg just ended!
Freiburg Galaxy becomes useGalaxy.euMarch 15, 2018 Freiburg devops
As part of our ongoing growth and development, Freiburg Galaxy is becoming useGalaxy.eu
Galaxy User Conference: a successful first dayMarch 15, 2018 Freiburg
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!
Propagating hashtags in a Galaxy historyMarch 9, 2018 Freiburg galaxy tools users software-release
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.
Map and identify phenotypic mutations in model organism genomesMarch 8, 2018 Freiburg tools
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.
ELIXIR Galaxy kick-off meeting 14.03.2018 in FreiburgFebruary 13, 2018 Freiburg
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.
Genome Annotation ReloadedFebruary 11, 2018 Freiburg tools
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.
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P FrameworkFebruary 1, 2018 Freiburg paper
Clemens and the GalaxyP team have published a new article about metaproteomics and Galaxy. [Learn more about it](https://www.mdpi.com/2227-7382/6/1/7).
We are now part of COST (CA16212)!January 30, 2018 Freiburg
We are part of COST Impact of Nuclear Domains On Gene Expression and Plant Traits
Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivoJanuary 30, 2018 Freiburg paper
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.
Next Galaxy Workshop on HTS data analysis in September 2018January 26, 2018 Freiburg training
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!
Galaxy Workshop - Registration is closed!January 18, 2018 Freiburg training
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.
Freiburg Galaxy Team has open positions!January 18, 2018 Freiburg
The Freiburg Galaxy Team is looking for 2 Postdoctoral researchers.
ASaiM - an environment to analyze intestinal microbiota dataJanuary 17, 2018 Freiburg tools
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.
High-resolution TADs reveal DNA sequences underlying genome organization in fliesJanuary 16, 2018 Freiburg paper
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!
Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes.January 13, 2018 Freiburg paper
“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.
ELIXIR Galxy Admin workshop in Oslo.January 12, 2018 Freiburg training
We had a very nice Galaxy Admin workshop in Oslo.
GraphClust - Scalable clustering and annotation of structured and functional RNAs in an accessible and interactive fashionDecember 30, 2017 Freiburg tools
HiCExplorer - a suite of tools for reproducible Hi-C data analysis, quality control and visualizationDecember 30, 2017 Freiburg tools
Post Mortem: 2h Tool Execution OutageDecember 11, 2017 Freiburg devops downtime
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 about the Galaxy Training material and community as a preprint on bioRXivNovember 30, 2017 Freiburg paper
Sex differences in peripheral not central immune responses to paininducing injuryNovember 28, 2017 Freiburg paper
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.
DNA methylation signatures follow preformed chromatin compartments in cardiac myocytesNovember 22, 2017 Freiburg paper
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.
Post Mortem: Upload and various tool failuresNovember 21, 2017 Freiburg devops
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.
Registration open for Galaxy HTS data analysis workshop 26.02.-02.03.2018November 17, 2017 Freiburg training
We are offering another Galaxy workshop on HTS data analysis. Please apply here.
Successful Server Hardware ImprovementsNovember 15, 2017 Freiburg devops
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.
90+ tools updatedNovember 8, 2017 Freiburg tools
We updated our tools stack - more than 90 tools were updated to newest versions!
Workshop on Provisioning of Virtual Research Environments and Data ManagementNovember 7, 2017 Freiburg training talk
Minimap2 mapper for noisy long read sequences (e.g. Nanopore, PacBio)November 4, 2017 Freiburg tools
Talk @ 5th early-stage researchers Next-Generation Sequencing SymposiumOctober 24, 2017 Freiburg talk
Joachim presented the developments of HiCExplorer at the 5th early-stage researchers Next-Generation Sequencing Symposium in Heidelberg.
Helping at the Software Carpentry workshop @ EMBL Heidelberg and Talk @ de.NBIerOctober 19, 2017 Freiburg training talk
Bérénice was helping Toby Hodges, Malvika Sharan and the other instructors for the Software Carpentry workshop organized at EMBL in Heidelberg.
MetaboFlow meeting (training and hackathon)October 17, 2017 Freiburg training hackathon
Björn participated to the Wellcome Trust funded MetaboFlow meeting (training and hackathon) in Birmingham.
Our paper "Practical computational reproducibility in the life sciences" on bioRXivOctober 11, 2017 Freiburg paper
VGCN: Rolling Replacement of Cloud Compute ResourcesSeptember 29, 2017 Freiburg devops
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.
deNBI Summer School - Computational genomics and RNA biologySeptember 29, 2017 Freiburg training
Björn was at the deNBI Summer School on Computational genomics and RNA biology organised by the RNA Bioinformatics center. He gave training on:
FIXED: upload jobs not scheduledSeptember 28, 2017 Freiburg devops
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.
New Paper on "Mitochondrial mutations in human cancer: Curation of translation"September 26, 2017 Freiburg paper
Maϊwen Caudron-Herger and Sven Diederichs published about “Mitochondrial mutations in human cancer: Curation of translation”.
End of our 5-day HTS Galaxy workshop in Freiburg, GermanySeptember 22, 2017 Freiburg training
After 5 days, our HTS Galaxy workshop in Freiburg is over.
We passed the 2.000.000th job!September 14, 2017 Freiburg jobs
Today our Galaxy server has calculated its 2.000.000th job! Thanks to all our users and people that have contributed to this project!
Fixed: Galaxy Metadata IssueAugust 31, 2017 Freiburg devops
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.
STAR: Ultrafast alignment of RNA-seq dataAugust 2, 2017 Freiburg tools
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.
W4M: Workflow4Metabolomics 3.0July 2, 2017 Freiburg tools
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.