Office of Advanced Research Computing

Amarel monthly maintenance
2021-06-15 08:00 - 2021-06-16 19:00, 2021-07-20 08:00 - 2021-07-21 19:00, 2021-08-17 08:00 - 2021-08-18 19:00, 2021-09-21 08:00 - 2021-09-22 19:00, 2021-11-16 08:00 - 2021-11-17 19:00, 2021-12-21 08:00 - 2021-12-22 19:00 (America/New_York)
Anticipated monthly maintenance schedule March 2021 - January 2022:
MAR 19-20-21 (3/20 & 3/21 Hill Data Center maintenance, which will affect Amarel users)
APR 20-21
MAY 18-19
JUN 15-16
JUL 20-21
AUG 17-18
SEP 21-22
OCT 19-20
NOV 16-17
DEC 21-22
JAN 18-19

Visit Amarel system status for more information

Intro to Amarel Cluster
2021-06-21 10:00 - 12:30
Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible. You must have an Amarel account set up before the workshop.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm. Alternatively, Windows 10 users can install the complete Windows Subsystem for Linux.
Workshop 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.
**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).
If you have questions or need help, please email Paul Arias.
Register to attend the workshop:

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Intro to Linux Command Line
2021-07-07 14:00 - 17:00, 2021-10-01 14:00 - 17:00
Register to attend this workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm. Alternatively, Windows 10 users can install the complete Windows Subsystem for Linux.
Workshop 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.
**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).
If you have questions or need help, please email Bala Desinghu.
Register to attend the workshop:

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Intro to the Amarel Cluster
2021-07-23 14:00 - 17:00, 2021-10-15 14:00 - 17:00
Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible. You must have an Amarel account set up before the workshop.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm. Alternatively, Windows 10 users can install the complete Windows Subsystem for Linux.
Workshop 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.
**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).
If you have questions or need help, please email Bala Desinghu.
Register to attend the workshop:

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Intro to Python
2021-08-06 14:00 - 17:00, 2021-10-29 14:00 - 17:00
Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm.
Workshop content: This three hour workshop focuses on learning the basics of python programming including data types, conditionals, functions, and python in HPC environment.
**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).
If you have questions or need help, please contact Bala Desinghu.

Register to attend the workshop:

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Python for Big Data
2021-08-20 14:00 - 17:00, 2021-11-05 14:00 - 17:00
Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm.
Workshop content: This three hour workshop focuses on learning the python tools and techniques to work with big data that demand CPU and memory. It covers the basics of Numpy, Pandas, Numba, and Dask.
**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).
If you have questions or need help, please contact Bala Desinghu.Register to attend the workshop:
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Machine Learning with Python and Scikit-Learn
2021-09-03 14:00 - 17:00, 2021-11-19 14:00 - 17:00
Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm.
Workshop content: In this three hour workshop, we will go through the basics of unsupervised and supervised methods, discuss some of the popular models such as Support Vector Machines, Decision Trees, and Random Forest, and show how these models work for classification and regression problems.
**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).
If you have questions or need help, please contact Bala Desinghu.

Register to attend the workshop:

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Deep Learning with Python and Keras
2021-09-17 14:00 - 17:00
Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm.
Workshop content: This three hour workshop focuses on learning the basics of Deep Learning with Python and Keras including data preparation, artificial neural networks (ANN), Convolutional Neural Networks (CNN), and Recurrent Neural Networks (RNN).
**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).
If you have questions or need help, please contact Bala Desinghu.Register to attend the workshop:
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Machine Learning Series by OARC—Random Forest Workshop
2021-09-28 13:00 - 16:00
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.
Amarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
If you have questions or need help, please contact Janet Chang.
Topics:
1. Introduction to Machine Learning (ML)

Big data and Machine Learning
Relate Machine Learning to other disciplines
Machine Learning algorithms
Classification and Regression

2. Understanding Random Forest (RF)

Applications of Random Forests
Why Random Forests
The Random Forest Algorithm
Fundamental concepts – ML, RF

3. Implementing Random Forest

Feature Importance and Feature Selection
Dealing with missing data, and imbalanced data
Best split of the node–node impurity

Over-fitting and underfitting
The model performance
The model interpretability

4. Lab Exercise
We will use cancer health data combined with gene expression data to build random forest models, predicting output variables. Both classifier and regressor will be addressed.
Lab 1, Set up, and launch R
Lab 2, Data preparation

2a. pre-processing,
2b. data partition,
2c. missing data imputation,
2d. feature selection

Lab 3, Building the RF model:

3b. handling imbalanced data
3c. building the RF model
3d. turning the parameters

Lab 4, Validation and model performance

4a. prediction and Confusion Matrix — test data
4b. ROC curve and AUC
4c. k-fold cross-validation
4d. parallel computing

Lab 5, Visualization and the model interpretation

5a. plotting the random forest tree
5b. plotting feature importance
5c. partial dependence plot (PDP)
5d. MDS – multi-dimensional scaling plot of proximity matrix

To Register:

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Clinical informatics – introduction
2021-09-29 13:00 - 15:00
Workshop 1: Clinical informatics, data science in biomedicine and Advanced computing seriesBranimir Ljubic presents the first workshop: “Clinical informatics – introduction” within the series of workshops: “Clinical informatics, Data science in medicine, Advanced computing.” These workshops will provide theoretical insights and practical advice needed for understanding and successful work in the field of Clinical informatics and Data science in medicine. The first workshop will cover the introduction to Clinical informatics, significance, modern applications, etc.
**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).
If you have questions or need help, please contact Branimir Ljubic.Register to attend the workshop:
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Clinical informatics, data science in biomedicine and Advanced computing series – workshop 2
2021-10-06 13:00 - 15:00
Workshop 2: Computer science in clinical medicine, introduction into Machine learning, Advanced machine learning methods in medicine — review
Branimir 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.
**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).
If you have questions or need help, please contact Branimir Ljubic.

Register to attend the workshop:

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HPC in life science—Genomics Series2, Variant analysis on Amarel cluster
2021-10-08 13:00 - 16:00
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.
Amarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
If you have questions or need help, please contact Janet Chang.
1. Introduction – The Basics of Variant Analysis

Concepts of genetic variant
The journey of variant study
Significance
Challenges

2. Variant Analysis –Overview

Workflow and informatics tools
Variant detection methods
Variant calling algorithms
Variant annotation and functional prediction
Variant prioritization, filtering, and validation

3. Variant Analysis – Getting ready

File format—fastq, vcf, bed, bam/sam
Variant ID and databases
Variant Reporting
Variant visualization
** Variant analysis of COVID-19 genomes

4. Variant calling pipeline example — GATK

GATK Best practices
Pre-processing

BWA, picard and GATK-format, Dealing with duplicates,
Base recalibration (BQSR)

Variant discovery

HaplotypeCaller, Germline and somatic mutation calling,
Variant recalibration (VQSR), Variant Filtering

Preliminary analysis

Variant annotation/function prediction
Variant evaluation

5. Variant calling pipeline example — Varscan2, Samtools

SNP/INDEL calling using Varscan2
SNP/INDEL calling using samtools/bcftools
Filtering and function prediction

6. Labs

Lab1 — Pre-processing, QC, mapping, and reference preparation
Lab2 — GATK pipeline
Lab3 — Samtools and varscan2 pipelines
Lab4 — Variant annotation/ Functional prediction
Lab5 — Visualization
Lab6 — Manage your jobs using slurm job scheduler

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Computer science in medicine, introduction into Machine learning, traditional learning models – workshop 3
2021-10-14 12:00 - 15:00
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.)
Branimir 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.
**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).
If you have questions or need help, please contact Branimir Ljubic.

Register to attend the workshop:

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Machine learning, Deep learning models (CNN, RNN, GAN) – workshop 4
2021-10-21 12:30 - 15:30
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.
**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).
If you have questions or need help, please contact Branimir Ljubic.Register to attend the workshop:
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Workshop 5. Social Networks (graphs) - theory and examples of medical applications
2021-12-02 13:00 - 16:00
Branimir Ljubic presents the workshop/seminar: “Social Networks (graphs) – theory and examples of medical applications” within the series of workshops/seminars: “Clinical informatics, Data science in medicine, Advanced computing.” This workshop/seminar will cover Social Networks (graphs).

Register to attend the workshop:

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Enabling protein structure prediction with artificial intelligence at Rutgers and beyond
2021-12-09 13:00 - 17:00
Learning objectives
This Institute for Quantitative Biomedicine Crash Course will present a broad overview of how Artificial Intelligence/Machine Learning (AI/ML) methods are being used for de novo protein structure prediction and provide hands-on experience with both AlphaFold2 and RoseTTAFold.
CASP14 revealed that AlphaFold2, developed by Google DeepMind, Inc., can predict three dimensional structures of small globular proteins with accuracies comparable to experimental methods. RoseTTAFold, developed at the University of Washington/Howard Hughes Medical Institute, approaches AlphaFold2 in terms of prediction accuracy while requiring fewer computational resources.
In this Crash Course, expert speakers will provide a solid foundation on the role of AI/ML in structural biology and showcase ongoing research efforts at Rutgers. During the hands-on tutorial, participants will learn how to utilize these new computational tools to compute structure models from amino acid sequences and download precomputed structure models from the AlphaFoldDB database. Local computing resources (Rutgers University Amarel Cluster) and access to Google Colab and the RoseTTAFold server will be made available during the hands-on session.
Co-organizers: Balamurugan Desinghu, Ph.D. and Stephen K. Burley, M.D., D.Phil
View schedule [PDF]
Register for event

Deep Learning with Python and Keras
2021-12-10 14:00 - 17:00
Register to attend the workshop at the bottom of this page. Zoom link will be emailed after filling out the registration form.
Amarel account: Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm.
Workshop content: This three hour workshop focuses on learning the basics of Deep Learning with Python and Keras including data preparation, artificial neural networks (ANN), Convolutional Neural Networks (CNN), and Recurrent Neural Networks (RNN).
**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).
If you have questions or need help, please contact Bala Desinghu.

Register to attend the workshop:

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Intro to Linux Command Line
2022-01-07 14:00 - 17:00
Amarel account: Apply here as soon as possible.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm. Alternatively, Windows 10 users can install the complete Windows Subsystem for Linux.
Workshop 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.
**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).
If you have questions or need help, please email Bala Desinghu.

Amarel monthly maintenance
2022-01-11 08:00 - 2022-01-12 19:00
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.
2022 anticipated maintenance schedule (all dates subject to change):
JAN 11 & 12
FEB 15 & 16
MAR 15 & 16
APR 19 & 20
MAY 17 & 18
JUN 21 & 22
JUL 19 & 20
AUG 16 & 17
SEP 20 & 21
OCT 18 & 19
NOV 15 & 16
DEC 20 & 21
Maintenance 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).

Visit Amarel system status for more information

Intro to the Amarel Cluster
2022-01-14 14:00 - 17:00
Amarel account: Apply here as soon as possible. You must have an Amarel account set up before the workshop.
VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.
SSH setup: Windows users must install an SSH client like PuTTY or MobaXterm. Alternatively, Windows 10 users can install the complete Windows Subsystem for Linux.
Workshop 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.
**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).
If you have questions or need help, please email Bala Desinghu.
