- Medbionode - MedUniGraz Mailing Lists

MedBioNode and RStudio operational again

by Trajanoski, Slave

Dear MedBioNode users, our MedBioNode cluster, as well as RStudio server are working again. Regards, Slave -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock 8010 Graz Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years

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Urgent!!!!!

by Trajanoski, Slave

Dear MedBioNode users, I’ve just received the information from IT department, that cooling system in the server rooms are not operational and to protect the MedBioNode cluster equipment we need to shut it down. These are very unfortunate, as well as unforeseeable circumstances that require immediate action. ############# Therefore MedBioNode cluster will be shut down in the next minutes!!!!!!!!!!!! ################# Thanks for your understanding!!!!! Regards, Slave -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock 8010 Graz Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years

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[WORKSHOP] 10x Genomics Data Analysis

by Durdevic, Marija

Dear researchers, If you want to get an overview of your 10X data before moving on to deeper bioinformatics research, please register for a free hands-on training at https://shorturl.at/5TbCL . You will learn the fundamentals of using Loupe Browser and Xenium Explorer to analyze 10x Genomics data without having to learn any coding languages. REGISTRATION & Program: https://shorturl.at/5TbCL Date: Tuesday, May 28, 2024 Time: 9:00h - 11:30h Loupe Browser Session 13:00h - 14:30h Xenium Explorer Session Venue: Seminar Room EG-086, ZMF ground floor, Stiftingtalstraße 24, 8036 Graz Bring your own laptop and learn how to do some basic analysis using Loupe Browser! Have a nice weekend, Marija Marija Đurđević, MSc PhD, Diagnostic & Research Center for Molecular BioMedicine Institute of Pathology Senior Bioinformatician, Core Facility Computational Bioanalytics Center for Medical Research Medical University Graz Center for Medical Research Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock A-8010 Graz Austria

2 years, 1 month

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Invitation for Austrian BioInformatics Workshop and ZMF 20th Anniversary

by Trajanoski, Slave

Sorry for my second E-Mail today, as well as I apologize to the ones receiving this invitation again!! Dear Sir or Madam! Dear MedBioNode User! We would like to invite you to the Austrian Bioinformatics Workshop on Wednesday, July 3rd, 2024 at the Medical University Graz. Please register and submit talks and posters on https://bioinformatik.at/workshop2024.<https://bioinformatik.at/workshop2024> For more information, visit Austrian Bioinformatics Workshop 2024 in Graz | Austrian Bioinformatics Platform (bioinformatik.at).<https://bioinformatik.at/workshop2024> We also cordially invite you to the ZMF 20th Anniversary on Thursday, July 4th / Friday, July 5th 2024 at the Medical University Graz. For organizational reasons we ask you to register via this link<https://www.medunigraz.at/events/detail/zmf-20th-anniversary> until June 14th, 2024. Best regards, Slave -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock 8010 Graz Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years, 2 months

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Information about running java jre on MedBioNode

by Trajanoski, Slave

Herewith I'd like to share important information with you. IT department was working on some slurm jobs issue and discovered that one needs to be aware of how java is handling "tmp" folder. Java is only honoring the $TMP environment variable on windows. On Linux Java is using a hardcoded "/tmp" when creating temporary file objects. It seems that the workaround for this is to set the java.io.tmp property of the JVM to the content of $TEMPDIR environment variable at startup like this: java -Djava.io.tmpdir="$TEMPDIR" ... For further information see this stackoverflow thread: https://stackoverflow.com/questions/1924136/environment-variable-to-control… Thanks for your attention -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock 8010 Graz Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years, 2 months

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login node sx036 reboot

by Trajanoski, Slave

Dear MedBioNode users, I’ve rebooted the login node and used this opportunity to also upgrade rstudio server to the latest version. Regards, Slave -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years, 4 months

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Login node sx036 restart

by Trajanoski, Slave

Dear MedBioNode users, login node sx036 lost connection to the mount point "/home/cluster" and therefore needs to be restarted. We plan to make the restart over the weekend, so please take this in consideration and expect short downtime. The reboot will also affect all RStudio Server users, since it is running on this machine. Running SLURM jobs will not be affected. Thanks for the understanding. Regards, Slave -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock 8010 Graz Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years, 4 months

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Cluster expansion

by Trajanoski, Slave

Dear MedBioNode user, it is planned in the next time to expand our HPC infrastructure and therewith to provide more CPU and GPU performance for jobs execution. To proper plan cluster growth it is very critical to evaluate your needs, as well as expected amount of future CPU based or GPU based data analysis tasks. Therefore provide us information about bottlenecks that you currently experience in using MedBioNode. Also it will be very helpful if you can already estimate calculation capacity separately CPU or GPU for your data analysis for this year. If you have some questions, or you're uncertain how to provide this information contact me to assist you. Thanks very much in advance for your cooperation. Best regards, Slave -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock 8010 Graz Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years, 4 months

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Singularity on MedBioNode

by Trajanoski, Slave

Dear MedBioNode users, I'd like to bring to your attention that we have Singularity version 4.0.3 on our cluster. Best regards, Slave -- Slave Trajanoski, Phd Senior Scientist Bioinformatics CF Computational Bioanalytics, Center for medical research Medical University Graz Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock 8010 Graz Tel. +43 316 385 73024 E-Mail: slave.trajanoski(a)medunigraz.at<mailto:slave.trajanoski@medunigraz.at>

2 years, 4 months

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Effective Use of COLOR in Your Science Visualization - a Crash Course

by Durdevic, Marija

Dear members of the MedBioNode, I apologize in advance for sending this email here since I am aware that it has nothing to do with the MedBioNode. Nonetheless, as I am aware that scientific visualization plays a crucial role in any data analysis, I would like to draw your attention to this and extend an invitation to attend an open lecture on "Effective Use of COLOR in Your Science Visualization - a Crash Course" featuring Dr. Jernej Zupanc<https://www.seyens.com/jernej-zupanc/>. Please refer to the information about the lecture that is attached to this email. We would be grateful if you could also let your colleagues know about this information. * DATE/ TIME: Feb 5th 2024, 9:00 - 10:00 * LOCATION: Aula, MedUni Graz * keynote lecture: Dr. Jernej Zupanc "Effective Use of COLOR in Your Science Visualization - a Crash Course" We are looking forward to seeing you on Feb 5th! On behalf of the organizing committee and MedBioNode, Marija Đurđević, MSc PhD, Diagnostic & Research Center for Molecular BioMedicine Institute of Pathology Senior Bioinformatician, Core Facility Computational Bioanalytics Center for Medical Research Medical University Graz Center for Medical Research Neue Stiftingtalstraße 6-West, Turm/Stiege:P, 4.Stock A-8010 Graz Austria

2 years, 5 months

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