News
Program for the Galaxy User Conference
Feb 13, 2018We 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.
Read moreDuring 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.
Read moreClemens and the GalaxyP team have published a new article about metaproteomics and Galaxy. Learn more about it.
Read moreCongratulation 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.
Read moreWe are now part of COST (CA16212)!
Jan 30, 2018We are part of COST Impact of Nuclear Domains On Gene Expression and Plant Traits
Read moreBecause 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!
Read moreFreiburg Galaxy Team has open positions!
Jan 18, 2018Due 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.
Read moreNew 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.
Read moreNew 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!
Read more“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.
Read moreRead more#oslo airport nailed it! #usegalaxy pic.twitter.com/vHh1nMehWK
— Björn Grüning (@bjoerngruening) January 13, 2018
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.
Read moreTomas 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:
Read moreOur 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.
Read moreCongrats 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.
Read moreCongrats 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.
Read moreYesterday (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.
Read moreLast 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.
Read moreWe updated our tools stack - more than 90 tools were updated to newest versions!
Read moreWe just updated our Galaxy server to version 17.09! Actually this was done by Eric Rasche, our new team member! Welcome Eric!
Read moreWorkshop on Provisioning of Virtual Research Environments and Data Management
Nov 7, 2017 training talkDo you have Nanopaore or PacBio reads? Try minimap2 as a new aligner! From minimaps homepage:
Read moreThanks to a contribution from Melanie Föll (Schilling Lab) we have added tools for analysing imaging mass spectrometry data.
Read moreRead moreMultiQC from @tallphil is available in #usegalaxy via IUC. Thanks to @Yvan2935 and EnginesOn! https://t.co/MwlsuRiKIx
— Bérénice Batut (@bebatut) 24 octobre 2017
Joachim presented the developments of HiCExplorer at the 5th early-stage researchers Next-Generation Sequencing Symposium in Heidelberg.
Read moreHelping at the Software Carpentry workshop @ EMBL Heidelberg and Talk @ de.NBIer
Oct 19, 2017 training talkRead moreDay 1 of #metaboflow's #usegalaxy workshop/hackathon with #Workflow4Metabolomics & @PhnmlH2020. #wellcometrust @ELIXIREurope #denbi pic.twitter.com/663oyxCVxM
— Ralf Weber (@ralf_weber) 16 octobre 2017
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.
Read moreRead more.@bjoerngruening talking about levels of reproducibility at the @biocontainers hackathon #biocon17 pic.twitter.com/qAnRHnnZke
— Rafael C Jimenez (@rafajido) 10 octobre 2017
Björn was at the deNBI Summer School on Computational genomics and RNA biology organised by the RNA Bioinformatics center. He gave training on:
Read moreA 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.
Read moreRead moreFinal day of our #usegalaxy workshop at @UniFreiburg. pic.twitter.com/IQX8hjYha1
— Björn Grüning (@bjoerngruening) 22 septembre 2017
Read morePresenting ASaiM during #GCB2017 #usegalaxy #metagenomics https://t.co/mgmLeSQA5J... Check out also our preprint https://t.co/OVsrH17pn6 pic.twitter.com/7w3F1W0vMi
— Bérénice Batut (@bebatut) 19 septembre 2017
Today our Galaxy server has calculated its 2.000.000th job! Thanks to all our users and people that have contributed to this project!
Read moreMany 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.
Read moreFor 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.
Read moreOur 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.
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