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PRODID:-//Office of Advanced Research Computing - ECPv6.0.10//NONSGML v1.0//EN
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X-ORIGINAL-URL:https://oarc.rutgers.edu
X-WR-CALDESC:Events for Office of Advanced Research Computing
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BEGIN:VTIMEZONE
TZID:America/New_York
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TZOFFSETFROM:-0500
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TZNAME:EDT
DTSTART:20210314T070000
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DTSTART:20211107T060000
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BEGIN:VEVENT
DTSTART;TZID=America/New_York:20211001T140000
DTEND;TZID=America/New_York:20211001T170000
DTSTAMP:20260421T104659
CREATED:20210813T001932Z
LAST-MODIFIED:20210813T001939Z
UID:5399-1633096800-1633107600@oarc.rutgers.edu
SUMMARY:Intro to Linux Command Line
DESCRIPTION:Register to attend this workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form. \nAmarel 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. \nRegister to attend the workshop:\n \n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/intro-to-linux-command-line-10-1-21/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20211006T130000
DTEND;TZID=America/New_York:20211006T150000
DTSTAMP:20260421T104659
CREATED:20210910T171908Z
LAST-MODIFIED:20210913T171314Z
UID:5633-1633525200-1633532400@oarc.rutgers.edu
SUMMARY:Clinical informatics\, data science in biomedicine and Advanced computing series – workshop 2
DESCRIPTION:Workshop 2: Computer science in clinical medicine\, introduction into Machine learning\, Advanced machine learning methods in medicine — review\nBranimir Ljubic presents the second workshop within the series of workshops: “Clinical informatics\, Data science in medicine\, Advanced computing.” The workshop will cover Prediction of medical conditions using Advanced Machine Learning (ML) Techniques — review of the newest methods and trends. Importance of the entire process of creating ML algorithms applicable in clinical medicine.  \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 contact Branimir Ljubic.\n\nRegister to attend the workshop:\n\n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/clinical-informatics-workshop2-10-6-21/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20211008T130000
DTEND;TZID=America/New_York:20211008T160000
DTSTAMP:20260421T104659
CREATED:20210813T200133Z
LAST-MODIFIED:20211108T204913Z
UID:5439-1633698000-1633708800@oarc.rutgers.edu
SUMMARY:HPC in life science—Genomics Series2\, Variant analysis on Amarel cluster
DESCRIPTION:Please register to attend this workshop at the bottom of this page. After filling out the registration form\, we will email you the Zoom link. \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. \nIf you have questions or need help\, please contact Janet Chang. \n1. Introduction – The Basics of Variant Analysis \n\nConcepts of genetic variant\nThe journey of variant study\nSignificance\nChallenges\n\n2. Variant Analysis –Overview \n\nWorkflow and informatics tools\nVariant detection methods\nVariant calling algorithms\nVariant annotation and functional prediction\nVariant prioritization\, filtering\, and validation\n\n3. Variant Analysis – Getting ready \n\nFile format—fastq\, vcf\, bed\, bam/sam\nVariant ID and databases\nVariant Reporting\nVariant visualization\n** Variant analysis of COVID-19 genomes\n\n4. Variant calling pipeline example — GATK \n\nGATK Best practices\nPre-processing\n\nBWA\, picard and GATK-format\, Dealing with duplicates\,\nBase recalibration (BQSR)\n\n\nVariant discovery\n\nHaplotypeCaller\, Germline and somatic mutation calling\,\nVariant recalibration (VQSR)\, Variant Filtering\n\n\nPreliminary analysis\n\nVariant annotation/function prediction\nVariant evaluation\n\n\n\n5. Variant calling pipeline example — Varscan2\, Samtools \n\nSNP/INDEL calling using Varscan2\nSNP/INDEL calling using samtools/bcftools\nFiltering and function prediction\n\n6. Labs \n\nLab1 — Pre-processing\, QC\, mapping\, and reference preparation\nLab2 — GATK pipeline\nLab3 — Samtools and varscan2 pipelines\nLab4 — Variant annotation/ Functional prediction\nLab5 — Visualization\nLab6 — Manage your jobs using slurm job scheduler\n\n \n\n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/hpc-life-science-genomics-series2-10-8-21/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20211014T120000
DTEND;TZID=America/New_York:20211014T150000
DTSTAMP:20260421T104659
CREATED:20210928T201809Z
LAST-MODIFIED:20210928T202934Z
UID:5778-1634212800-1634223600@oarc.rutgers.edu
SUMMARY:Computer science in medicine\, introduction into Machine learning\, traditional learning models  – workshop 3
DESCRIPTION:Workshop 3: Computer science in medicine\, introduction into Machine learning\, traditional learning models (Decision trees\, K-NN\, Perceptron\, SVM\, Bagging – Boosting (random forest\, Adaboost)\, etc.)\nBranimir Ljubic presents the third workshop: “Computer science in medicine\, introduction into Machine learning\, traditional learning models (Decision trees\, K-NN\, Perceptron\, SVM\, Bagging – Boosting (random forest\, Adaboost)\, etc.)” within the series of workshops: “Clinical informatics\, Data science in medicine\, Advanced computing.” The third workshop will cover traditional Machine Learning methods. \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 contact Branimir Ljubic.\n\nRegister to attend the workshop:\n\n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/clinical-informatics-workshop3-10-14-21/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20211015T140000
DTEND;TZID=America/New_York:20211015T170000
DTSTAMP:20260421T104659
CREATED:20210813T005354Z
LAST-MODIFIED:20210813T005429Z
UID:5404-1634306400-1634317200@oarc.rutgers.edu
SUMMARY:Intro to the Amarel Cluster
DESCRIPTION:Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form. \nAmarel 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. \nRegister to attend the workshop:\n\n\n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/intro-to-the-amarel-cluster-10-15-21/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20211021T123000
DTEND;TZID=America/New_York:20211021T153000
DTSTAMP:20260421T104659
CREATED:20211012T205356Z
LAST-MODIFIED:20211012T205402Z
UID:5855-1634819400-1634830200@oarc.rutgers.edu
SUMMARY:Machine learning\, Deep learning models (CNN\, RNN\, GAN) – workshop 4
DESCRIPTION:Branimir Ljubic presents the fourth workshop: “Machine learning\, Deep learning models (CNN\, RNN\, GAN)” within the series of workshops: “Clinical informatics\, Data science in medicine\, Advanced computing.” This workshop will cover Deep learning Machine learning methods. \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 contact Branimir Ljubic.Register to attend the workshop:\n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/machine-learning-deep-learning-models-cnn-rnn-gan-workshop-4/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/New_York:20211029T140000
DTEND;TZID=America/New_York:20211029T170000
DTSTAMP:20260421T104659
CREATED:20210813T025400Z
LAST-MODIFIED:20210813T025406Z
UID:5409-1635516000-1635526800@oarc.rutgers.edu
SUMMARY:Intro to Python
DESCRIPTION:Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form. \nAmarel 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. \nWorkshop content: This three hour workshop focuses on learning the basics of python programming including data types\, conditionals\, functions\, and python in HPC environment. \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 contact Bala Desinghu.\n\nRegister to attend the workshop:\n\n	Notice: JavaScript is required for this content.
URL:https://oarc.rutgers.edu/event/intro-to-python-10-29-21/
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