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X-WR-CALNAME:Office of Advanced Research Computing
X-ORIGINAL-URL:https://oarc.rutgers.edu
X-WR-CALDESC:Events for Office of Advanced Research Computing
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TZID:America/New_York
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TZOFFSETFROM:-0500
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TZNAME:EDT
DTSTART:20220313T070000
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DTSTART:20221106T060000
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BEGIN:VEVENT
DTSTART;TZID=America/New_York:20220107T140000
DTEND;TZID=America/New_York:20220107T170000
DTSTAMP:20260406T231154
CREATED:20211130T153520Z
LAST-MODIFIED:20221128T152923Z
UID:6142-1641564000-1641574800@oarc.rutgers.edu
SUMMARY:Intro to Linux Command Line
DESCRIPTION:Amarel account: Apply here as soon as possible. \nVPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources. \nSSH setup: Windows users must install an SSH client like PuTTY or MobaXterm. Alternatively\, Windows 10 users can install the complete Windows Subsystem for Linux. \nWorkshop content: This 3-hour workshop offers a brief introduction to using the Linux operating system\, focusing on command-line operations. The primary objective is to provide beginner-level familiarity with using a Linux system for common research computing tasks. Linux systems (e.g.\, workstations\, remote servers\, computing clusters) can be thought of as the foundation of research computing. \n**Note** Just observing is welcome\, but to participate in hands-on activities\, you must have an Amarel account setup before the workshop. Please complete our web-based form at least 24 hours before the workshop (do this as soon as possible). \nIf you have questions or need help\, please email Bala Desinghu.
URL:https://oarc.rutgers.edu/event/intro-to-linux-command-line-1-7-22/
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BEGIN:VEVENT
DTSTART;TZID=America/New_York:20220111T080000
DTEND;TZID=America/New_York:20220112T190000
DTSTAMP:20260406T231154
CREATED:20210416T184318Z
LAST-MODIFIED:20220105T215347Z
UID:4736-1641888000-1642014000@oarc.rutgers.edu
SUMMARY:Amarel monthly maintenance
DESCRIPTION:Each maintenance period is expected to begin at about 08:00 ET on the first day and end by about 19:00 ET on the 2nd day. \n2022 anticipated maintenance schedule (all dates subject to change):\nJAN 11 & 12 \nFEB 15 & 16\nMAR 15 & 16\nAPR 19 & 20\nMAY 17 & 18\nJUN 21 & 22\nJUL 19 & 20\nAUG 16 & 17\nSEP 20 & 21\nOCT 18 & 19\nNOV 15 & 16\nDEC 20 & 21 \nMaintenance is usually scheduled for weekdays because it often involves coordination with University facilities teams or external vendors. There may also be times when Amarel must be unavailable due to externally-scheduled data center facilities\, power\, or telecommunications maintenance. When this happens\, we will do our best to avoid adding to a month’s downtime with our own maintenance work (e.g.\, by working in parallel or postponing some tasks). \n			\n				Visit Amarel system status for more information
URL:https://oarc.rutgers.edu/event/amarel-monthly-maintenance-1-11-22/
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BEGIN:VEVENT
DTSTART;TZID=America/New_York:20220114T140000
DTEND;TZID=America/New_York:20220114T170000
DTSTAMP:20260406T231154
CREATED:20211130T155415Z
LAST-MODIFIED:20221128T153020Z
UID:6145-1642168800-1642179600@oarc.rutgers.edu
SUMMARY:Intro to the Amarel Cluster
DESCRIPTION:Amarel account: Apply here as soon as possible. You must have an Amarel account set up before the workshop.  \nVPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources. \nSSH setup: Windows users must install an SSH client like PuTTY or MobaXterm. Alternatively\, Windows 10 users can install the complete Windows Subsystem for Linux. \nWorkshop content: This fast-paced 3-hour short course offers a brief introduction to using a Linux cluster. The goal is to help everyone make those first few steps toward productively using a Linux cluster for research — all members of the Rutgers community have free access to the Amarel Cluster. The workshop covers the basics of HPC Cluster\, Web access to the cluster\, SLURM\, File System and Storage\, and Setting up environment for the Software Stacks. \n**Note** Just observing is welcome\, but to participate in hands-on activities\, you must have an Amarel account setup before the workshop. Please complete our web-based form at least 24 hours before the workshop (do this as soon as possible). \nIf you have questions or need help\, please email Bala Desinghu.
URL:https://oarc.rutgers.edu/event/intro-to-the-amarel-cluster-1-14-22/
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BEGIN:VEVENT
DTSTART;TZID=America/New_York:20220121T130000
DTEND;TZID=America/New_York:20220121T163000
DTSTAMP:20260406T231154
CREATED:20211108T212521Z
LAST-MODIFIED:20221128T153404Z
UID:6030-1642770000-1642782600@oarc.rutgers.edu
SUMMARY:RNA-Seq workshop Part 1
DESCRIPTION:Computational Genomics Series by OARC \nAmarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible. \nVPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources. \nTo connect to the cluster: Please test and be sure it is working for you. Check the user-guide of how to get on to the cluster. \nIf you have questions or need help\, please contact Janet Chang. \n\nIntroduction to RNA-Seq\n\nIssues to consider\nExperimental design\n(read length\, depth\, replicates..)\nStatistics for RNASeq – power analysis\n\n\nQC and Raw read QC\n\nDaily utilities\nFastq QC and Interpretation\nQuality trim-Trimmomatics\n\n\nRead mapping and Read counts\n\nAligners—tophat\, bowtie\, bwa\, Star\, HISAT2\,\nSalmon\nHtSeq-count/STAR quantMode geneCounts…\nPost mapping QC\n\n\n\nLab Exercise: FastQC; seqtk; Trimmomatic; HISAT2;
URL:https://oarc.rutgers.edu/event/rna-seq-workshop-part-1/
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BEGIN:VEVENT
DTSTART;TZID=America/New_York:20220124T130000
DTEND;TZID=America/New_York:20220124T163000
DTSTAMP:20260406T231154
CREATED:20211108T221526Z
LAST-MODIFIED:20221128T153516Z
UID:6046-1643029200-1643041800@oarc.rutgers.edu
SUMMARY:RNA-Seq workshop part 2
DESCRIPTION:Computational Genomics Series by OARC \nAmarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible. \nVPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources. \nTo connect to the cluster: Please test and be sure it is working for you. Check the user-guide of how to get on to the cluster. \nIf you have questions or need help\, please contact Janet Chang. \n\nData processing and filtering\n\nIntroduction to R and Bioconductor\nData processing–filtering\nNormalization\n\n\nQuantification and Differential expression\n\nExpression Quantification\nStatistical Models\nMultiple test correction\n\n\nAnalysis QC (Sample QC)\n\nClustering\nPCA\nHeatmap\nVolcano plot\n\n\n\nLab Exercise: data preparation; DE analysis with edgeR;\nPCA\, Clustering\, heatmap\, Volcano plot…
URL:https://oarc.rutgers.edu/event/rna-seq-workshop-part-2/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20220128T130000
DTEND;TZID=America/New_York:20220128T163000
DTSTAMP:20260406T231154
CREATED:20211109T134130Z
LAST-MODIFIED:20221128T153850Z
UID:6057-1643374800-1643387400@oarc.rutgers.edu
SUMMARY:RNA-Seq workshop part 3
DESCRIPTION:Computational Genomics Series by OARC \nAmarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible. \nVPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources. \nTo connect to the cluster: Please test and be sure it is working for you. Check the user-guide of how to get on to the cluster. \nIf you have questions or need help\, please contact Janet Chang. \n\nFunctional analysis\n\nGO Term Annotation and Enrichment Test\nGene Set Enrichment Analysis and GSEA\nOverview of Pathway analysis\nOverview of Co-expression/network analysis\n\n\nID mapping & conversion\n\ng:profiler\nEnsembl Biomart\nSynergizer\nPICR\n\n\nVisualization\n\nLab Exercise: GO analysis\, GSEA analysis\, term\nconversion; IGV\, SparK
URL:https://oarc.rutgers.edu/event/rna-seq-workshop-part-3/
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