Remote training using GalaxySeptember 15, 2020 Freiburg training
The COVID-19 pandemic at the beginning of 2020 forced us to rethink and restructure our training offerings to do more remote training. We aimed for a scalable, flexible and open-for-all workshop experience.
Enough talking - time to act!🌍🔥 September 11, 2020 Freiburg s4f
September the 25th will see the next global climate strike! As last time, the Freiburg Galaxy Team is going to express its support more directly:
The ELIXIR tools platform for COVID-19 research at the ECCB2020September 10, 2020 Freiburg talk
The 19th European Conference on Computational Biology is now over. The research on COVID-19 that is being carried out since February was presented in the session “A glimpse into Global Bioinformatics Communities: Europe - ELIXIR”.
EOSC-Life has awarded two training projects to the European Galaxy teamSeptember 8, 2020 Freiburg training grants
Within the 1st EOSC-Life Training Open Call, two out of four proposals have been awarded to the European Galaxy team to develop climate science e-learning material and mentoring and training opportunities for our communities.
Freiburg Galaxy team is participating to the 2nd cohort of the Open Life Science programSeptember 7, 2020 Freiburg training
Open Life Science (OLS) is an online mentoring & training program to help individuals and stakeholders in research to become Open Science ambassadors.
New Paper on "No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics"September 2, 2020 Freiburg paper
The scientific efforts to fight the current COVID-pandemic have yielded plenty of data. Unfortunately, this data is not always fully shared. In this publication, we show how to overcome these limitations by providing an open platform for transparent research.
New Paper on "pyGenomeTracks: reproducible plots for multivariate genomic data sets"September 1, 2020 Freiburg paper
We are happy to announce the publication of pyGenomeTracks (PGT) in Bioinformatics. The tool plots combinations of genomic tracks in a modular way and it’s available on the European Galaxy server. Many thanks to all the authors for the great effort!
New Paper on "Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera"August 31, 2020 Freiburg paper
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies.
New Paper on "An epigenetic map of malaria parasite development from host to vector"August 30, 2020 Freiburg paper
The malaria parasite replicates asexually in the red blood cells of its vertebrate host employing epigenetic mechanisms to regulate gene expression in response to changes in its environment. We used chromatin immunoprecipitation followed by sequencing in conjunction with RNA sequencing to create an epigenomic and transcriptomic map of the developmental transition from asexual blood stages to male and female gametocytes and to ookinetes in the rodent malaria parasite Plasmodium berghei.
Galaxy: the first 10,000 pubsAugust 27, 2020 Freiburg paper
We reached 10,000 publications in the Galaxy Publication Library this month. This library tracks publications that use, extend, implement or reference Galaxy or Galaxy-based platforms. It includes journal articles, theses, book chapters, preprints, and a couple more odds and ends. This milestone is a good opportunity to look at what the library tells us about where the Galaxy project has been, and maybe where it’s going as well.
Galaxy will join the NFDI-DataPLANT consortium in October 2020August 22, 2020 Freiburg
Starting in October 2020 until September 2025, the European Galaxy team in Freiburg will participate in the consortium DataPLANT for the development of a service and data infrastructure designed to record and deliver large data volumes for modern crop research funded by the German Research Foundation (DFG).
3 steps to get your tool into Galaxy - A real-world exampleAugust 22, 2020 Freiburg
In this blog post, we will explain how you can get your software tool into a Galaxy server and with this, exposed to thousands of researchers.
For this purpose, we will follow David’s steps to add the very generic UNIX
diff tool to Galaxy.
Galaxy Africa Community UpdateJuly 30, 2020 Freiburg training tiaas gcc
During the July virtual meet-up of the Bioinformatics Hub of Kenya (BHKi), a training on Galaxy was conducted by Peter van Heusden (SANBI) with 72 attendees registered from many different countries: Cote d’Ivoire, India, Kenya, Mali, Saudi Arabia, South Africa, Sudan, Tanzania, Uganda, …
UseGalaxy.eu update to 20.05July 29, 2020 Freiburg release
We’ve updated our Galaxy server to version 20.05. This version includes the migration to Python 3 and improves usability in the aspects listed below.
Climate Science at BCC2020July 27, 2020 Freiburg
July has been a very busy month for Galaxy Climate ending with several sessions dedicated to Climate Science at BCC2020. It started on July 18-19 with two introductory training sessions (West and East) on “Getting your hands on Climate data” where attendees learned on accessing and analyzing climate data in Galaxy. One important aspect was to explain the difference between climate and weather data; show how to visualize climate data on a map with Galaxy and then how to create and share a simple workflow for framing a very simple adaptation case study. This event was supported by Galaxy Europe and TIaaS and benefited from the allocation of completely dedicated compute resources for the duration of the training.
Training Infrastructure Feedback from Rodrigo Ortega PoloJuly 25, 2020 Freiburg training tiaas
An introductory workshop to bacterial whole-genome sequence analysis was delivered from December 9-12, 2019 in the Lethbridge Research and Development Centre (Agriculture and Agri-Food Canada). There were 7 participants which included a research scientist (PI), a visiting scientist, a research technician, a postdoctoral fellow, and three graduate students.
Computational chemistry at BCC2020July 23, 2020 Freiburg
Several sessions were related to computational chemistry during this year’s BCC. On July 18th we ran a successful introductory tutorial on ‘Intuitive, reproducible high-throughput molecular dynamics in Galaxy’. The online training was led jointly by representatives from the European Galaxy Team (Simon Bray) and the University of Cape Town (Chris Barnett, Tharindu Senapathi).
The landscape of SARS-CoV-2 RNA modificationsJuly 19, 2020 Freiburg paper
Nanopores are an awesome technology! We already gained experiences with it in our StreetScience project, where we show citizens and school kids what DNA sequencing is, how they can sequence with a USB-like device (Minion) and how they can analyze the data with Galaxy. But Nanopores can also sequence RNAs directly. Direct RNA Sequencing (DRS) can detect RNA modification in high-throughput!
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorialJuly 3, 2020 Freiburg training
Update: The paper is now published in the Journal of Cheminformatics.
Processing of Single Cell RNA-Seq Data with GalaxyJuly 3, 2020 Freiburg training
We will be hosting a single-cell RNA-seq training workshop at BCC, on both July 17th and July 19th for BCC 2020. The workshop follows the 10x-driven workflows as outlined in our preprint ‘A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework’, and will be given by members of the European Galaxy Team (Mehmet Tekman and Björn Grüning) and the Friedrich Miescher Institute for Biomedical Research (Hans-Rudolf Hotz).
Training Infrastructure Feedback from Marcel SchulzJune 8, 2020 Freiburg training tiaas
Galaxy helps virtual teaching!
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platformJune 3, 2020 Freiburg paper
We are happy to announce a new publication, ‘The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform’ in the Journal of Cheminformatics. This accompanies our Galaxy webserver for computational chemistry, located at https://cheminformatics.usegalaxy.eu.
Galactic May NewsMay 14, 2020 Freiburg galaxy
The May 2020 Galactic News is out!
Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and explorationApril 23, 2020 Freiburg paper
Proteogenomics, enables new insights into understanding the complex biological systems by integrating genomics/transcriptomics with mass spectrometry based proteomics data. It is a powerful approach to extract direct evidence of expression of novel protein sequences specific to a sample of interest. The importance of proteogenomics studies is reflected in the field of cancer and other genetic diseases.
Integrative meta-omics analysis - Metagenomics, Metatranscriptomics, MetaproteomicsApril 14, 2020 Freiburg tools
James Taylor (1979-2020)April 3, 2020 Freiburg
We just lost James Taylor (1979-2020). His legacy — open, reproducible science — will continue.
Workshop on Workflow Management SystemsApril 2, 2020 Freiburg training
Representatives from five RIs presented exemplary cases on typical image analysis pipelines during the first day. The second day started with an introduction to EOSC-Life and the tools roadmap, followed by the presentations of the different Workflow Management Systems. Later, each participant had the opportunity to attend a breakout session to ask questions to the experts.
ChiRA tool suite - an integrated framework for Chimeric Read Analysis from RNA-RNA interactome dataMarch 24, 2020 Freiburg tools
ChiRA is a set of tools to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, LIGR-Seq, etc.
Scientific Infrastructure for Virus ResearchMarch 24, 2020 Freiburg de.NBI ELIXIR eosc
Data and analyses relating to SARS-CoV-2 are available on the University of Freiburg’s Galaxy platform.
WirVsVirus HackathonMarch 19, 2020 Freiburg hackathon
We want to encourage you to participate and join the fight against Covid-19.
Virtual screening against SARS-CoV-2 main proteaseMarch 11, 2020 Freiburg tools
Thanks to some amazing work done at the Diamond Light Source in the UK, protein structures of SARS-CoV-2 main protease in complex with a number of different fragments have recently been published.
Storage issues and potential data lossMarch 9, 2020 Freiburg devops
On Friday, we unfortunately experienced some data loss. Currently, we believe that some datasets created in the last two months were affected.
de.NBI Training Infrastructure Feedback from Helena RascheMarch 6, 2020 Freiburg training tiaas denbi
We just wrapped up the Galaxy Admin Training week in Barcelona, Spain.
Open collaborative infrastructure to tackle public health emergenciesFebruary 28, 2020 Freiburg de.NBI ELIXIR
The rapid spread of the COVID-19 virus highlights the need for an open analytics environment so that the global research community can collaborate on developing effective countermeasures.
Coronavirus data analysis by University of FreiburgFebruary 26, 2020 Freiburg de.NBI ELIXIR
The Galaxy platform enables the free and transparent overview of COVID-19 genome informations. For more information also visit https://covid19.galaxyproject.org.
Crowdsourcing citizen science data on usegalaxy.euFebruary 25, 2020 Freiburg de.NBI
Galaxy for Ecology, mixing Ecology research, Citizen Science and Massively Multi Online Science by Yvan Le Bras, Simon Bénateau.
12,000 users - 6,900,000 jobs - 13,300,000 datasetsFebruary 12, 2020 Freiburg report
In the next days we will attend our yearly de.NBI SAB meeting. Time to look at some statistics.
New Paper on "Gene expression in immortalized versus primary isolated cardiac endothelial cells"February 11, 2020 Freiburg paper
Congratulation to Achim Lother and colleagues to their great publication! And thanks a lot for using the European Galaxy server for your data analysis. We are happy that it was helpful.
Exciting progress in the ELIXIR Galaxy communityFebruary 11, 2020 Freiburg galaxy elixir
ELIXIR has published a progress report about the ELIXIR Galaxy community in 2020! Thanks a lot to the entire Galaxy world-wide Galaxy community, without this all would not be possible!
Training Infrastructure Feedback from Beata ScholtzFebruary 10, 2020 Freiburg training tiaas
I am an associate professor at the Faculty of Medicine, University of Debrecen, Hungary, and I have been using the Galaxy platform to teach the basics of RNA-seq data analysis to 2nd year Molecular Biology MSc students since 2016. The goal of my course is to help students move from the concept of “RNA-seq is awesome, it gives us lots of data” to a solid understanding of how the sequencing process works, how the raw data looks like, and how we can get from the raw reads to the heart of the biological processes.
CORBEL staff visit program: Integration IDR - GalaxyFebruary 8, 2020 Freiburg tools
As part of the training program in Work Package 9, CORBEL offers staff visits across research infrastructures. In this frame, EuroBioimaging and ELIXIR members met during three days with the European Galaxy team in Freiburg (Germany) to make image data from the Image Data Resource (IDR) accessible through the Galaxy interface.
Galaxy provides support as an NFDIFebruary 7, 2020 Freiburg
Germany wants to build a national research data infrastructure NFDI which can systematically manage scientific and research data, provide long-term data storage, backup and accessibility, and network the data both nationally and internationally. The University of Freiburg applied as a lead with the “DataPLANT” project to connect plant researchers in Germany and to provide a suitable infrastructure for data analysis.
Accessible and reproducible mass spectrometry imaging data analysis in GalaxyFebruary 6, 2020 Freiburg paper
Congratulation to our friend and colleague Melanie Föll from the University of Freiburg Oliver Schilling lab to her great article on the analysis of mass spectrometry imaging data. She has integrated 18 tools dedicated to mass spectrometry imaging into our Galaxy framework. Thanks a lot for making your tools available to the proteomics and imaging community!
ELIXIR tools platform meeting and Container SIS meeting in ParisJanuary 30, 2020 report
Galaxy Training SurveyJanuary 29, 2020 Freiburg galaxy training
We need your feedback!
Outreach - Invited Talk for Introducing Galaxy to Uniklinik FreiburgJanuary 22, 2020 Freiburg talk
We were invited by Dr. Achim Lother (AG Cardiovascular Pharmacology, Uniklinik Freiburg) and Prof. Christoph Bode for a talk about introducing Galaxy and RNAseq data analysis to researchers of the Uniklinik Freiburg. Anika presented Galaxy as a framework to allow researchers without any programming or informatics skills to perform their own data analysis. 30 scientists and researchers attended the talk, picked flyers and got information about upcoming Galaxy workshops. We are happy to support our local Freiburg community!
Training Infrastructure Feedback from Denny PoppJanuary 20, 2020 Freiburg training tiaas
For a 1-day course on long read sequencing for (meta)genomics I was looking for a powerful, easy-to-use computational infrastructure.
Human multi-omics data from UK Personal Genome Project accessible through UseGalaxy.euJanuary 16, 2020 Freiburg training pgp open-data
Galactic January NewsJanuary 8, 2020 Freiburg galaxy
The January 2020 Galactic News is out!
Survey of metaproteomics software tools for functional microbiome analysisJanuary 8, 2020 Freiburg paper
Our metaproteomics and microbiomics communities are constantly growing. This article on bioRxiv may be interesting for many of you: “Survey of metaproteomics software tools for functional microbiome analysis”. The authors compare six open software tools for microbiome analysis, including Unipept 4.0 and eggNOG-mapper, which are already installed in the European Galaxy framework.
Massively Multiplayer Online Science in Galaxy to help Ecologists - a citizen science project.January 7, 2020 Freiburg galaxy mmos devops
A few years back the “webhook” concept was contributed to the Galaxy codebase. Webhooks have enabled custom modifications to the Galaxy User Interface (UI) without changing the Galaxy source code directly. The advantage is that the maintenance of custom changes is a lot easier. You can think of it as a plugin concept for the Galaxy UI. Webhooks are powering the so much-loved XKCD or PhD comics that you see when you submit jobs or workflows for example - but this was just the first step…
Laborjournal article about GalaxyJanuary 5, 2020 Freiburg paper
The Laborjournal is a German journal for scientists for complex methods and news written in easily understandable language. Björn from our team was interviewed about Galaxy in life science. The article is in German - you can practice your German skills ;-)
118 new plant reference genomes and transcriptomes added to Galaxy Europe!January 5, 2020 Freiburg tools
In cooperation with our ELIXIR partner in Belgium, the VIB, we have recently added more than 100 new plant reference genomes and transcriptomes to the European Galaxy server. These reference datasets are obtained from PLAZA, a platform for comparative plant genomics, with the help of the Belgian Galaxy team led by Frederik Coppens. The PLAZA Data Warehouse provides access to the parsed and curated data, through an FTP-server and API, which is leveraged to provide, and in the future keep up-to-date, the plant genomes for the Galaxy Community.
Training Infrastructure Feedback from the Gallantries ProjectDecember 10, 2019 Freiburg training tiaas
The Gallantries Project recently had their final meeting in Thessaloniki, Greece!
Training Infrastructure Feedback from Ambre JousselinDecember 3, 2019 Freiburg training tiaas
At the end of November, we organized a 2-day workshop (reads quality, short and long reads genome assembly, reads mapping and RNAseq differential gene expression) for 12 master students.
10,000 users, 6.370.000 jobs and 11.900.000 datasetsDecember 2, 2019 Freiburg devops
This week we have reached a huge milestone!
Training Infrastructure Feedback from Giovanni WidmerDecember 1, 2019 Freiburg training tiaas
Hi Galaxy team!
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIRNovember 30, 2019 Freiburg paper training
The Galaxy Team is part of the German Network of Bioinformatics infrastructure (de.NBI) and ELIXIR, both networks have a strong focus on training and education. As you know we are passionate about training life scientists in data analysis and offer hundrets of workshops and the infrastructure to scale your training with TIaaS. Now, de.NBI has published a paper to introduce our activities within these large networks. Enjoy reading!
GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clusteringNovember 30, 2019 Freiburg paper
Going back to the roots of the Prof. Backofen lab, our colleague Milad has published a paper on annotation and discovery of structured RNAs with scalable and accessible integrative clustering with GraphClust2. We are happy that we were able to support Milad to integrate GraphClust2 into Galaxy and make it available to our RNA community. Congratulations to Milad and colleagues!
Enough talking - time to act!🌍🔥 November 23, 2019 Freiburg s4f
November 29 will see the next global climate strike and this time The Freiburg Galaxy Team is going to express its support more directly:
gProfiler is published and running on usegalaxy.euNovember 20, 2019 Freiburg tools
gProfiler is a toolset for functional enrichment analysis and conversions of gene lists.
Galactic November NewsNovember 16, 2019 Freiburg galaxy
The November 2019 Galactic News is here!
SINA available in Galaxy - Accurate high-throughput multiple sequence alignment of ribosomal RNA genesNovember 11, 2019 Freiburg tools
SILVA Incremental Aligner (SINA) is avaiable in Galaxy!
UseGalaxy – a bioinformatic shopping mall from Sivakumar PrakashNovember 8, 2019 Freiburg
Sivarkumar is working at the Centre for Cellular and Molecular Biology (CCMB) on de novo genome assembly of Capparis urophylla. We received his feedback and want to share it with you. Thanks a lot for using Galaxy, Sivakumar!
RNA-Seq Training feedback from Simon MoxonNovember 7, 2019 Freiburg training tiaas
I am an associate professor at the University of East Anglia in the UK and I have been wanting to teach undergraduate biology students some practical skills in next generation sequencing analysis since I started my position in 2016. I was put off by having to teach all of the prerequisites required such as using the Linux command line, working with R etc. There was also a real reluctance from the students to learn these more technical skills and I didn’t want risk alienating them before we even started looking at any sequencing data. Another big barrier for us was the difficulty in setting up accounts for 60 undergrads on our HPC facilities so I had to find an alternative method for teaching.
Training update from Tomas KlingströmNovember 2, 2019 Freiburg training tiaas
In a world where climate zones are changing it is absolutely critical for agricultural scientists to collaborate across borders. In this case an NRF-STINT grant to support collaboration between South Africa and Sweden has allowed us to dive deeper into suitable touch points for collaboration between the South African Agricultural Research Council (ARC) and the Swedish University of Agricultural sciences. As a Swedish researcher working with the development of infrastructure for automatic data collection on dairy cattle farms (the Gigacow infrastructure) and infectious diseases entering Europe (the Defend2020 project) this is a great opportunity to learn more about the work on ARC. More specifically I was visiting the Animal Production Unit where my partner in NRF-STINT Dr Avhashoni Zwane is employed and with ARC-Onderstepoort Veterinary Research (OVR) campus which is also a partner in the Defend 2020 project.
Use the power of pandas / numpy to transform tabular datasets in a myriad of ways with our new Table Compute tool.October 23, 2019 Freiburg tools
With Table Compute you can:
- drop or duplicate given rows or columns from a tabular dataset
- filter rows or columns on their properties
- replace or transform table elements
- compute tables of summary statistics across rows or columns
Parent instance errorOctober 18, 2019 Freiburg devops bug
UseGalaxy.eu is currently facing some issues with tools execution and it may take us a while to find a solution.
If you get an error message of this kind:
Parent instance <ToolShedRepository at 0x7fe3f20dca10> is not bound to a Session; lazy load operation of attribute 'tool_dependencies' cannot proceed (Background on this error at: http://sqlalche.me/e/bhk3)
Training Infrastructure Feedback from Charles GirardotOctober 15, 2019 Freiburg training tiaas
In early September this year, the European Molecular Biology Laboratory (EMBL) organized a week long course entitled Chromatin Signatures During Differentiation: Integrated Omics. This high-quality course was limited to 16 participants and gathered scientists from all around the world.
UseGalaxy.eu Upgrading to 19.09October 2, 2019 Freiburg devops downtime
We will upgrade to 19.09 tomorrow morning at 9am local time (2019-10-03 09:00:00 CEST). We expect the process to take ~1 hour.
Galactic October NewsOctober 2, 2019 Freiburg galaxy
The October 2019 Galactic News is here!
Another successful Galaxy high-throughput data analysis workshop in FreiburgSeptember 30, 2019 Freiburg training
Last week, the Freiburg Galaxy team taught another Galaxy workshop on HTS data analysis. It takes place every year in February and September in Freiburg. In an intense full week, we are teaching for Galaxy beginners in a real hands-on training course the use of Galaxy and its application in data analysis of RNAseq, ChIPseq, HiC, and DNA methylation. We tested the new computer rooms in the city center of Freiburg and found them really nice (a CIP pool with daylight!). In this workshop, we had 29 particpants from Germany and Europe.
8000 users, 6.000.000 jobs and 11.000.000 datasetsSeptember 17, 2019 Freiburg devops
Scientists must act on our own warnings to humanity🌍🔥 September 16, 2019 Freiburg s4f
From a recent Nature article:
The European Galaxy server is part of the EOSC marketplaceSeptember 15, 2019 Freiburg tools
Since a few days, the European Galaxy server is part of the European Open Science Cloud marketplace. The Freiburg Galaxy team is an official EOSC member and are helping researchers worldwide.
Galactic September NewsAugust 30, 2019 Freiburg galaxy
The September 2019 Galactic News is here!
PathwayMatcher published and running on usegalaxy.euAugust 20, 2019 Freiburg tools
PathwayMatcher builds a protein-protein interaction network from the Reactome pathway database. Users can query this network with multiple types of omics data as input, and PathwayMatcher outputs the possibly affected biochemical reactions, subnetworks, and pathways.
Slamdunk - SLAMseq analysis for nucleotide-conversion sequencing datasetsAugust 17, 2019 Freiburg tools
Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretation of such events in high-throughput sequencing datasets demands specialized bioinformatics approaches.
Galaxy Community Conference - a brief summary!August 6, 2019 Freiburg training tiaas gcc
The 2019 Galaxy Community Conference (GCC2019) was held in Freiburg, Germany, 1-8 July. 2019 was the largest GCC ever with 231 participants, 39 Galaxy training courses, 65 talks, 54 posters, 13 demos, and more than 30 different BoFs. Our participants came from 27 different countries of Eastern- and Western Europe, North America, Asia, Oceania and Sub-saharan Africa.
The Galaxy Genome Annotation Project - Scaling Genome Annotation for the MassesAugust 5, 2019 Freiburg tools
The Galaxy Genome Annotation (GGA) Project is focused on supporting genome annotation inside Galaxy. It consists of several teams, projects, and tool suites that are working closely together to deliver a comprehensive, scalable and easy to use Genome Annotation experience. This blog post will highlight a few of the recent developments and the new Genome Annotation subsection of the European Galaxy server: https://annotation.usegalaxy.eu
MaxQuant goes GalaxyAugust 2, 2019 Freiburg tools
After lots of requests for a more up-to-date MaxQuant tool it finally is there! The European Galaxy server now contains two MaxQuant tools. One features options for SILAC and label free quantification and also the possibility to process fractioned data by uploading an experimental design template. The other one operates on a parameter file uploaded by the user. This enables the usage of all the features of MaxQuant, but might be less convenient to use.
Galactic NewsAugust 1, 2019 Freiburg galaxy
The August 2019 Galactic News is here!
The European Galaxy Team with talks at ISMB/ECCBJuly 22, 2019 Freiburg talk
We were invited in July to give talks at the ISMB/ECCB organized by the International Society for Computational Biology. During the ELIXIR-hosted special session on “Scalable Plant-Research in Cloud Environments” we presented “Galaxy and the European Galaxy Community”, “Apollo and Galaxy”, and “e!DAL”. We spent a really great day in Basel (CH).
Galactic NewsJuly 1, 2019 Freiburg galaxy
The July 2019 Galactic News is here!
GCC2019 will be livestreamedJune 30, 2019 Freiburg release talk video
This year’s GCC is live streamed! If you couldn’t make it to Germany, come check out some of the talks and trainings taking place in Freiburg this week.
Tool Recommendation: What do I do next?June 27, 2019 Freiburg devops release
If you’ve done interactive data analysis, it’s likely at least once you were faced with the question “What do I do next?” Maybe you’re following the publicly available parts of a protocol, maybe you’re doing a novel analysis, maybe you just want to add a new graph and some extra pizzaz to the reporting workflow you built for your project.
TIaaS Queue StatusJune 17, 2019 Freiburg devops
A common request during trainings was “how are the students doing, are they finished with the current step?” This is a common question, especially given some of the sleepy grad students trainees at 9am. For our TIaaS users, we have added a brief overview of the training queue, showing them at a glance if everyone is finished with the current step.
Native support for Elixir-AAI in Galaxy v.19.05June 13, 2019 Freiburg release
As of Galaxy version 19.05 released last month, Galaxy can easily be configured to use Elixir-AAI service for authenticating users! As the first publicly available Galaxy instance, the European Galaxy Server hosted by Elixir Germany is now ready to accept logins from users using their Elixir AAI identity for authentication.
Training Infrastructure Feedback from Nevena VeljkovicJune 10, 2019 Freiburg training tiaas
In the spring semester, the Molecular Biology, a three-year PhD programme by the Faculty of Biology in Belgrade offered an elective course Genomics. This year 7 students attended this course.
Galactic NewsJune 1, 2019 Freiburg galaxy
The June 2019 Galactic News is here! This is a summary of what is going on in the Galaxy community.
Queue changes during GCCMay 24, 2019 Freiburg devops
As Freiburg is hosting the Galaxy Community Conference this year, we will be allocating a lot of extra resources for training and events during the conference. To accomplish this, we will decrease the size of the main queue, and re-allocate these resources to the conference. You may notice that jobs take longer to run in the weeks before/during/after the conference, please be patient with us during this time. After the conclusion of the conference things will return to normal.
Another successful Galaxy workshop in MelbourneMay 20, 2019 Freiburg training tiaas
Recently we ran another Galaxy workshop using UseGalaxy.eu’s Training infrastructure as a Service (TIaaS). The workshop was an “Introduction to Galaxy and RNA-seq” run over two afternoons at the Peter MacCallum Cancer Centre in Melbourne, Australia. The attendees were a mix of students and postdocs and their feedback was good, they liked the hands-on, practical nature of the course. Thanks to the Galaxy EU team for enabling the course through providing the convenience of the TIaaS service.
The RNA workbench 2.0: next generation RNA data analysisMay 10, 2019 Freiburg paper
Galactic NewsMay 1, 2019 Freiburg galaxy
The May 2019 Galactic News is here! This is a summary of what is going on in the Galaxy community.
A successful tool and training workshop for the ELIXIR Galaxy Community at RoscoffApril 26, 2019 Freiburg training
Last week, the ELIXIR Galaxy Community organized a 4-days workshop related to Galaxy tool integration and training. This event was hosted by the Biological station of Roscoff, in the (sunny/rainy) beautiful Brittany (France).
GCC registration is open and abstracts can be submitted until FridayApril 24, 2019 Freiburg training
GCC2019 will be held 1-8 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. 2019 also brings the most significant conference program update in several years! Find out more on the event page.
Visit from Macromolecular Crystallography Group (Diamond Synchrotron)April 23, 2019 Freiburg collaboration
Recently, we have started working with the Macromolecular Crystallography group, which is based at the Diamond synchrotron in Didcot, UK. We have a common interest in enabling reproducible, user-friendly data analysis in cheminformatics and computational chemistry. As part of their XChem project, they are developing computational workflows to assist in designing follow-up compounds from fragment screening hits. Diamond is working with Informatics Matters to develop Squonk, a computational notebook with similar aims to the ChemicalToolbox we are working on. We were interested in investigating how Squonk and Galaxy could be integrated.
A sneak peak at the Galaxy Community Conference 2019 in Freiburg!April 4, 2019 Freiburg gcc2019
As you probably know GCC2019 will be held in Freiburg, Germany, from 1-6 July. Like previous Galaxy Community Conferences, GCC2019 will feature keynotes, accepted talks, posters, and demos, birds-of-a-feather gatherings, multiple days of collaborative work, and plenty of opportunities to network with your fellow data-intensive researchers and practitioners. If you are working in data-intensive life science, there is no better place to be.
BeerDEcoded: 1st public workshopApril 4, 2019 Freiburg streetscience
On the 31st of March, we held our first public workshop for the BeerDEcoded project in Freiburg. Several students and external people participated in this event, making a total of 16 people, including us.
We passed the 5.000.000th jobs and 5.000 users!April 3, 2019 Freiburg devops
Galactic NewsApril 1, 2019 Freiburg galaxy
The April 2019 Galactic News is here! This is a summary of what is going on in the Galaxy community.
Convert mass spectrometry data file formats with msconvertMarch 24, 2019 Freiburg release
msconvert is a tool to convert mass spectrometry data file formats.
New Paper on "Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315"March 20, 2019 Freiburg paper
Jonna E. Teikari et al. published about the “Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315”.
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!
Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clusteringFebruary 21, 2019 Freiburg paper
Our paper “Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clustering” is now available as preprint on bioRXiv. Congratulation to Milad and co-authors!
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.
HiC Workshop for INDEPTH in LucerneOctober 10, 2018 Freiburg training
Successful Galaxy Proteomics workshop in PragueOctober 5, 2018 Freiburg training
Together with members from the ELIXIR Czechia node, we have carried out a 2-days Galaxy Proteomics workshop from 4th to 5th of October in Prague, Czech Republic. We had 25 participants from the life science field and focused on proteomics tools available for Galaxy and development of workflows to combine processing steps.
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.
Galaxy and ... Bioconda, CLIP Explorer and RNA workbench @ GCB 2018September 25, 2018 Freiburg
During the German Conference on Bioinformatics in Vienna, we presented our work related to Galaxy. Read here the abstracts:
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.
Galaxy on de.NBI cloud now with more powerSeptember 1, 2018 Freiburg devops
We are one out of five German de.NBI cloud centers that provides storage and compute resources for the life science community. Thanks to a new de.NBI grant, the European Galaxy Server now has extended CPU memory and storage resources. Expect less waiting time in the queue, smoother big training events and more power for your research!
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.
New paper "Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization"March 6, 2018 Freiburg paper
Melanie and colleagues published a paper on “Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization”. Thank you for using Galaxy and congratulation to the authors!
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.