Office of Advanced Research Computing

Deep Learning with Python and Keras
2021-12-10 14:00 - 17:00 (America/New_York)
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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Amarel monthly maintenance
2021-12-21 08:00 - 2021-12-22 19:00
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 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, 2022-03-15 08:00 - 2022-03-16 19:00, 2022-05-17 08:00 - 2022-05-18 19:00, 2022-06-21 08:00 - 2022-06-22 19:00, 2022-07-19 08:00 - 2022-07-20 19:00, 2022-08-16 08:00 - 2022-08-17 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, 2022-05-06 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.

RNA-Seq workshop Part 1
2022-01-21 13:00 - 16:30
Computational Genomics Series by OARC
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.
To 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.
If you have questions or need help, please contact Janet Chang.

Introduction to RNA-Seq

Issues to consider
Experimental design
(read length, depth, replicates..)
Statistics for RNASeq – power analysis

QC and Raw read QC

Daily utilities
Fastq QC and Interpretation
Quality trim-Trimmomatics

Read mapping and Read counts

Aligners—tophat, bowtie, bwa, Star, HISAT2,
Salmon
HtSeq-count/STAR quantMode geneCounts…
Post mapping QC

Lab Exercise: FastQC; seqtk; Trimmomatic; HISAT2;

RNA-Seq workshop part 2
2022-01-24 13:00 - 16:30
Computational Genomics Series by OARC
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.
To 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.
If you have questions or need help, please contact Janet Chang.

Data processing and filtering

Introduction to R and Bioconductor
Data processing–filtering
Normalization

Quantification and Differential expression

Expression Quantification
Statistical Models
Multiple test correction

Analysis QC (Sample QC)

Clustering
PCA
Heatmap
Volcano plot

Lab Exercise: data preparation; DE analysis with edgeR;
PCA, Clustering, heatmap, Volcano plot…

RNA-Seq workshop part 3
2022-01-28 13:00 - 16:30
Computational Genomics Series by OARC
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.
To 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.
If you have questions or need help, please contact Janet Chang.

Functional analysis

GO Term Annotation and Enrichment Test
Gene Set Enrichment Analysis and GSEA
Overview of Pathway analysis
Overview of Co-expression/network analysis

ID mapping & conversion

g:profiler
Ensembl Biomart
Synergizer
PICR

Visualization

Lab Exercise: GO analysis, GSEA analysis, term
conversion; IGV, SparK

Intro to Python
2022-02-04 14:00 - 17:00, 2022-05-20 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.
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.

Amarel monthly maintenance
2022-02-15 08:00 - 2022-02-16 19:00, 2022-04-19 08:00 - 2022-04-20 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 (one week earlier)
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

Python for Big Data
2022-02-18 14:00 - 17:00, 2022-06-03 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.
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.

Machine Learning with Python and Scikit-Learn
2022-03-11 14:00 - 17:00, 2022-06-10 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.
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.

Intro to Amarel Cluster
2022-03-24 14:00 - 17:00, 2022-04-05 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 Paul Arias.

Deep Learning with Python and Keras
2022-03-25 14:00 - 17:00, 2022-06-15 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.
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.

Data Visualization with Python
2022-04-08 12:30 - 14:30
Data Visualization with Python Jupyter Notebooks: A Hands-on Introduction
Presenters: Dr. Bala Desinghu, Dr. Abhishek Tripathi and Dr. Jim Samuel
The session will consist of brief presentations, with around 100 minutes of interactive work-along demo of data visualization with Jupyter Notebooks, and end with Q&A. Participants will learn to create data visualizations and can opt to either access Rutgers University’s high-performance computing (HPC) platform/cloud or to run the code locally on their own computers.

Dr. Bala Desinghu, Senior Scientist from OARC, Rutgers University will provide an interactive introduction to data visualization with insights on the use of high-performance computing.
Dr. Abhishek Tripathi, Associate Professor, School of Business, TCNJ, will introduce the use of Python libraries such as Seaborn, Plotly and Cufflinks for creating advanced and intera​ctive data visualizations.
Dr. Jim Samuel, Associate Prof​e​ssor, Rutgers Bloustein School, will conclude the session with insights on the use of Artificial Intelligence for visualizations and language data visualizations.

This workshop is hosted by the RUCI Lab, EJ Bloustein School and the Office of Advanced Research Computing (OARC), Rutgers University, organized by Dr. Bala Desinghu and Dr. Jim Samuel in collaboration with our partners, the Eastern Regional Network (ERN), the Northeast Big Data Innovation Hub (NEBDI Hub), and the New Jersey Big Data Alliance (NJBDA).
This workshop is sponsored by the MPI (Master of Public Informatics) Program at Bloustein.

Register here

AI for Protein Design - AlphaFold2 and RoseTTAFold
2022-04-22 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 workshop will present a broad overview and hands-on session on 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.
**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.

Intro to Linux Command Line
2022-05-13 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.
Register to attend the workshop:

Data Visualization with Python
2022-05-27 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.
Workshop content: This workshop provides hands-on training on how to utilize packages like numpy, pandas, matplotlib, plotly, etc. to store, process, and visualize data.
**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.
