Tags¶
Following is a list of relevant tags:
ACCESS¶
AI¶
AMD¶
Agentic AI¶
- Acceptable Use & Etiquette
- Agentic AI
- Best Practices & Limitations
- Context Files (/etc/agents.d)
- Harness Settings & Permissions
- Local (over SSH)
- MCP Servers
- On the Cluster (Login Nodes)
- Running Agents
- Shared Context & Settings
Anaconda¶
Annotation¶
Anvil¶
- API
- Access
- Access to Anvil
- Anvil Composable Subsystem
- Anvil Kubernetes
- Anvil Notebook
- Anvil Object Storage
- Anvil Software
- Anvil User Guide
- AnvilGPT on Anvil
- Chat Interface
- Concepts
- Examples
- File Management
- Frequently Asked Questions
- Getting Started
- Getting Started
- Getting Started
- Groups and Sharing
- Hosted Models
- Job Submission
- Key Policies
- MCP Integration
- Object Storage Concepts
- Overview
- Security and Access Control
- System Architecture
- Tool Calling
- User Tools
- Workspace
Anvil Cloud¶
Anvil Composable¶
AnvilGPT¶
- API
- AnvilGPT on Anvil
- Chat Interface
- Groups and Sharing
- Hosted Models
- MCP Integration
- Tool Calling
- Workspace
Apptainer¶
Assembly¶
Bell¶
- Accounts
- Ansys Fluent
- Apptainer
- Archive and compression
- Bell Overview
- Bell User Guide
- Biocontainers
- Biography of Bell
- Cancelling job
- Case Calculating with Fluent
- Checking Job Status
- Checking output
- Cluster Tools
- Command line
- Compiling Source Code
- Compute Node Desktop
- Directives
- Distributed Computing Server (parallel job)
- Environment variables
- Example Python Jobs
- Example: Create and Use Biopython Environment with Conda
- File Storage and Transfer
- Files
- Flost
- Fluent Text User Interface and Journal File
- Frequently Asked Questions
- Ftp sftp
- GROMACS
- Gateway (Open OnDemand)
- Gaussian
- Generic SLURM Jobs
- Globus
- Hadoop
- Holding job
- Home directory
- Hsi
- Htar
- Hybrid
- Implicit Parallelism
- Installing Packages
- Installing Packages from Source
- Installing R packages
- Intel mkl
- Interactive Apps
- Interactive Jobs
- Job Submission Script
- Job dependencies
- Jobs
- Jupyter Notebook
- Loading Data into R
- Long term storage
- Lost File Recovery
- MATLAB
- MPI
- Mac
- Managing Environments with Conda
- Managing Packages with Pip
- Manual
- Mathematica
- Matlab
- Matlab Script (.m File)
- Menu Launcher
- Monitoring Resources
- Mpi
- Multiple Node
- Numpy Parallel Behavior
- Octave
- OpenMP
- Openmp
- Parallel Computing Toolbox (parfor)
- Parallel Toolbox (spmd)
- Preparing Case Files for Fluent
- Profile Manager
- Python
- Queues
- R
- RStudio
- RStudio Server
- Rocmcontainers
- Running Jobs
- Running R jobs
- Running RStudio Server on Bell
- Scp
- Scratch space
- Serial
- Serial Jobs
- Setting Up R Preferences with .Rprofile
- Sharing
- Simple Job
- Software
- Spark
- Specific Applications
- Specific Types of Nodes
- Storage quota
- Submitting Fluent jobs to SLURM
- Submitting a Job
- Tensorflow
- Tmp directory
- Windows
- Windows
- Windows network drive
Box Research Lab Folder¶
Composable¶
Conda¶
Data Depot¶
- Access Permissions and Directories
- Archive and Compression
- Common Scenarios
- Data Depot User Guide
- Default Configuration
- File Storage and Transfer
- File Transfer
- Frequently Asked Questions
- Lost File Recovery
- Mac OS X
- Manual Browsing
- Overview
- Scheduling recurring Globus transfers between scratch and Data Depot
- Sharing Files
- Unix Groups
- Windows
- flost Tool
Data Management¶
Docker¶
Documentation¶
Fairuse¶
Fortress¶
- Accounts
- FTP / SFTP
- File Storage and Transfer
- File Transfer
- Fortress User Guide
- Frequently Asked Questions
- Globus
- HSI
- HTAR
- Overview
- Sharing Files
GPU¶
Gautschi¶
- Accounts
- Ansys Fluent
- Apptainer on Gautschi Cluster
- Archive and compression
- Biography of Gautschi
- Cancelling job
- Case Calculating with Fluent
- Checking output
- Cluster Tools
- Compile gpu
- Compile hybrid
- Compile mpi
- Compile openmp
- Compile serial
- Compiling Source Code
- Creating the Slurm Job Submission Script
- Distributed Computing Server (parallel job)
- Distributed Training on RCAC Clusters
- Environment variables
- Example Python Jobs
- File Storage and Transfer
- Files
- Flost
- Fluent Text User Interface and Journal File
- Frequently Asked Questions
- Ftp sftp
- GPU
- Gateway (Open OnDemand)
- Gaussian
- Gautschi Overview
- Gautschi User Guide
- Gautschi's Universal Software Launcher
- Generic SLURM Jobs
- Globus
- Holding job
- Home directory
- Hsi
- Htar
- Implicit Parallelism
- Installing R Packages
- Interactive Apps
- Job dependencies
- Jobs
- Loading Data into R
- Long term storage
- Lost File Recovery
- MPI
- Mac
- Manual
- Matlab
- Matlab Script (.m File)
- Monitoring GPU Usage
- Monitoring Resources
- Monitoring the Job
- Multiple Node Job
- OpenMP
- Parallel Computing Toolbox (parfor)
- Parallel Toolbox (spmd)
- Preparing Case Files for Fluent
- Profile Manager
- Python examples on Gautschi
- R examples on Gautschi
- RStudio
- Running Jobs
- Running R Jobs
- Running Serial Jobs
- Running interactive jobs on Gautschi
- SLurm Directives
- Scp
- Scratch space
- Setting up R Preferences with .Rprofile
- Sharing
- Simple Jobs
- Slurm accounts, partitions, and QOS options
- Software
- Storage quota
- Submitting Fluent jobs to SLURM
- Submitting a Job
- Tmp directory
- Using AI Agents
- Windows
- Windows network drive
Geddes¶
- API
- Access
- Biography of Lanelle Geddes
- Chat Interface
- Concepts
- Database
- Examples
- Geddes User Guide
- Groups and Sharing
- Hosted Models
- MCP Integration
- Overview of Geddes
- Purdue GenAI Studio
- R Shiny
- Registry
- Services
- Storage
- Tool Calling
- Troubleshooting
- Web Server
- Workloads
- Workspace
Genomics Exchange¶
- Genomics Exchange
- Genomics Exchange — Spring 2026
- Genomics Exchange, Fall 2026
- HPC Orientation for Biologists
- Nextflow on Gautschi
- Project Organization
- Publication-Quality Plots
- QC for Genomics
- R Skills for Biological Data
- Reproducible Genomics
- Running Bioinformatics on RCAC
- Session 1: Introduction & HPC Orientation
- Session 1: Reproducible Genomics Kickoff
- Session 2: Data Management for Biologists
- Session 2: Project Organization
- Session 3: Nextflow Fundamentals
- Session 3: R Data Wrangling
- Session 4: Publication-Quality Plots
- Session 4: Running nf-core Pipelines
- Session 5: Running Bioinformatics on RCAC
- Session 5: Script to pipeline
- Session 6: QC for Genomics
- Session 6: nf-core on Open OnDemand
- Session 7: R & Bioconductor on RCAC Clusters
- Session 7: Reproducible Bioinformatics with Nextflow
- Session 8: AI for Biologists
Gilbreth¶
- Accounts
- Ansys Fluent
- Apptainer on Gilbreth Cluster
- Archive and compression
- Biography of Gilbreth
- Cancelling job
- Case Calculating with Fluent
- Checking Job Status
- Checking output
- Cluster Tools
- Compile gpu
- Compile hybrid
- Compile intel mkl
- Compile mpi
- Compile openmp
- Compile serial
- Compiling Source Code
- Compute Node Desktop
- Custom ML Packages
- Directives
- Distributed Computing Server (parallel job)
- Environment variables
- Example Jobs
- Example Python Jobs
- Example: Create and Use Biopython Environment with Conda
- File Storage and Transfer
- Files
- Flost
- Fluent Text User Interface and Journal File
- Frequently Asked Questions
- Ftp sftp
- GPU
- GPU Usage Monitoring
- Gateway (Open OnDemand)
- Gaussian
- Generic SLURM Jobs
- Gilbreth Overview
- Gilbreth User Guide
- Globus
- Holding job
- Home directory
- Hsi
- Htar
- Implicit Parallelism
- Installing Packages
- Installing Packages from Source
- Installing R Packages
- Interactive Apps
- Interactive Jobs on Gilbreth
- Job Submission Script
- Job dependencies
- Jobs
- Jupyter Notebook
- Loading Data into R
- Long term storage
- Lost File Recovery
- MATLAB
- ML Batch Jobs
- MPI
- Mac
- Managing Environments with Conda
- Managing Packages with Pip
- Manual
- Matlab
- Matlab Script (.m File)
- Monitoring Resouces
- Multiple Node
- Numpy Parallel Behavior
- OpenMP
- Parallel Computing Toolbox (parfor)
- Parallel Toolbox (spmd)
- Preparing Case Files for Fluent
- Profile Manager
- Python examples on Gilbreth
- R examples on Gilbreth
- RStudio
- RStudio Server
- Running Jobs
- Running R jobs
- Scp
- Scratch space
- Serial Jobs
- Setting Up R Preferences with .Rprofile
- Sharing
- Simple Job
- Slurm accounts, partitions, and QOS options
- Software
- Storage quota
- Submitting Fluent jobs to SLURM
- Submitting a Job
- Tmp directory
- Using AI Agents
- Windows
- Windows network drive
Globus¶
Guides¶
- Downloading SRA Data
- HPC Orientation for Biologists
- Installing Perl Libraries
- Installing R Packages
- Nextflow and nf-core
- Nextflow on Gautschi
- Optimizing Trinity
- Productivity Tips
- Project Organization
- Publication-Quality Plots
- QC for Genomics
- R Skills for Biological Data
- Reproducible Genomics
- Running Bioinformatics on RCAC
- Scheduling recurring Globus transfers between scratch and Data Depot
- Transfer Data with iRODS
- VISPR Visualization
- VS Code on RCAC
HPC¶
- Getting Started with Bioinformatics and Computing at RCAC
- HPC Orientation for Biologists
- Optimizing Trinity
- Running Bioinformatics on RCAC
- Session 1: Introduction & HPC Orientation
- Session 1: Reproducible Genomics Kickoff
- Session 5: Running Bioinformatics on RCAC
- VS Code on RCAC
Hammer¶
- Accounts
- Apptainer
- Archive and compression
- Cancelling job
- Checking Job Status
- Checking output
- Command line
- Compiling Source Code
- Custom ML Packages
- Directives
- Distributed Computing Server (parallel job)
- Environment variables
- Example Python Jobs
- Example: Create and Use Biopython Environment with Conda
- File Storage and Transfer
- Flost
- Frequently Asked Questions
- Ftp sftp
- Gaussian
- Generic SLURM Jobs
- Globus
- Hammer Overview
- Hammer User Guide
- Holding job
- Home directory
- Hsi
- Htar
- Implicit Parallelism
- Installing Packages
- Installing Packages from Source
- Installing R packages
- Intel mkl
- Interactive Jobs
- Job Submission Script
- Job dependencies
- Loading Data into R
- Long term storage
- Lost File Recovery
- ML Batch Jobs
- ML-Toolkit
- MPI
- Mac
- Machine Learning
- Managing Environments with Conda
- Managing Packages with Pip
- Manual
- Mathematica
- Matlab
- Matlab Script (.m File)
- Menu Launcher
- Monitoring Resources
- Mpi
- Multiple Node
- Numpy Parallel Behavior
- Octave
- OpenMP
- Openmp
- Parallel Computing Toolbox (parfor)
- Parallel Toolbox (spmd)
- Profile Manager
- Python
- Queues
- R
- RStudio
- Running Jobs
- Running R jobs
- Running RStudio Server on Bell
- Scp
- Scratch space
- Serial
- Serial Jobs
- Setting Up R Preferences with .Rprofile
- Sharing
- Simple Job
- Software
- Specific Applications
- Specific Types of Nodes
- Storage quota
- Submitting a Job
- Tmp directory
- Windows
- Windows
- Windows network drive
Hands-On Workshops¶
Intel¶
Kubernetes¶
Life Sciences¶
- BRAKER3
- Downloading SRA Data
- GeMoMa
- Genomics Exchange
- Genomics Exchange — Spring 2026
- Genomics Exchange, Fall 2026
- Getting Started with Bioinformatics and Computing at RCAC
- HPC Orientation for Biologists
- Helixer
- HiFiasm (HiFi reads)
- Installing Perl Libraries
- Installing R Packages
- Juicer
- Life Sciences
- Mitochondrial Genomes (MitoHiFi)
- Nextflow and nf-core
- Nextflow on Gautschi
- Optimizing Trinity
- Productivity Tips
- Project Organization
- Publication-Quality Plots
- QC for Genomics
- R Skills for Biological Data
- RCAC Hands-On Bioinformatics Workshops
- RNA-seq
- Reproducible Genomics
- Running Bioinformatics on RCAC
- Scheduling recurring Globus transfers between scratch and Data Depot
- Session 1: Introduction & HPC Orientation
- Session 1: Reproducible Genomics Kickoff
- Session 2: Data Management for Biologists
- Session 2: Project Organization
- Session 3: Nextflow Fundamentals
- Session 3: R Data Wrangling
- Session 4: Publication-Quality Plots
- Session 4: Running nf-core Pipelines
- Session 5: Running Bioinformatics on RCAC
- Session 5: Script to pipeline
- Session 6: QC for Genomics
- Session 6: nf-core on Open OnDemand
- Session 7: R & Bioconductor on RCAC Clusters
- Session 7: Reproducible Bioinformatics with Nextflow
- Session 8: AI for Biologists
- Single-Cell RNA-seq
- Transfer Data with iRODS
- VISPR Visualization
- VS Code on RCAC
Login¶
MatPlotLib¶
- Advanced Plotting
- Animations
- Colormaps
- Envision Center
- Getting Started
- MatPlotLib Workshop Index Page
- Our First Script
- The Second Script
- Types of Plots
NAIRR¶
NVIDIA¶
Negishi¶
- Accounts
- Ansys Fluent
- Apptainer on Negishi Cluster
- Archive and compression
- BioContainers Collection
- Biography of Negishi
- Build your own VASP 5
- Build your own VASP 6
- Cancelling job
- Case Calculating with Fluent
- Checking output
- Cluster Tools
- Command line
- Compiling Source Code
- Compute Node Desktop
- Creating the Slurm Job Submission Script
- Distributed Computing Server (parallel job)
- Environment variables
- Example Python Jobs
- Example: Create and Use Biopython Environment with Conda
- File Storage and Transfer
- Files
- Flost
- Fluent Text User Interface and Journal File
- Frequently Asked Questions
- Ftp sftp
- Gateway (Open OnDemand)
- Gaussian
- Generic SLURM Jobs
- Globus
- Holding job
- Home directory
- Hsi
- Htar
- Hybrid
- Implicit Parallelism
- Installing Packages
- Installing Packages from Source
- Installing R Packages
- Intel mkl
- Interactive Apps
- Job Submission Matrix
- Job dependencies
- Jobs
- Jupyter Notebook
- Loading Data into R
- Long term storage
- Lost File Recovery
- MATLAB
- MPI
- Mac
- Managing Environments with Conda
- Managing Packages with Pip
- Manual
- Matlab
- Matlab Script (.m File)
- Menu Launcher
- Monitoring Resources
- Monitoring the Job
- Mpi
- Multiple Node Job
- Negishi Overview
- Negishi User Guide
- Numpy Parallel Behavior
- OpenMP
- Openmp
- Parallel Computing Toolbox (parfor)
- Parallel Toolbox (spmd)
- Preparing Case Files for Fluent
- Profile Manager
- Python examples on Negishi
- R examples on Negishi
- RStudio
- RStudio Server
- Running Jobs
- Running R Jobs
- Running Serial Jobs
- Running interactive jobs on Negishi
- SLurm Directives
- Scp
- Scratch space
- Serial
- Setting up R Preferences with .Rprofile
- Sharing
- Simple Jobs
- Slurm accounts, partitions, and QOS options
- Software
- Specific Types of Nodes
- Storage quota
- Submitting Fluent jobs to SLURM
- Submitting a Job
- Tmp directory
- Using AI Agents
- VASP
- VASP Job Submit Script
- Windows
- Windows
- Windows network drive
Nextflow¶
- Nextflow and nf-core
- Nextflow on Gautschi
- Session 3: Nextflow Fundamentals
- Session 4: Running nf-core Pipelines
- Session 5: Script to pipeline
- Session 6: nf-core on Open OnDemand
- Session 7: Reproducible Bioinformatics with Nextflow
Notebook¶
Object Storage¶
- Access
- Anvil Object Storage
- Getting Started
- Object Storage Concepts
- Security and Access Control
- User Tools
Performance¶
Profilers¶
- AMD uProf
- Intel VTune
- NVIDIA Nsight Systems
- NVIDIA Nsight Tools Overview
- NVIDIA Nsight Tools on RCAC Clusters
- Profilers
Purdue GenAI Studio¶
- API
- Chat Interface
- Groups and Sharing
- Hosted Models
- MCP Integration
- Purdue GenAI Studio
- Tool Calling
- Workspace
Python¶
- Advanced Plotting
- Animations
- Colormaps
- Envision Center
- Example Python Jobs
- Example Python Jobs
- Example Python Jobs
- Example: Create and Use Biopython Environment with Conda
- Getting Started
- Installing Packages
- Installing Packages from Source
- Job Submission
- Managing Environments with Conda
- Managing Packages with Pip
- MatPlotLib Workshop Index Page
- Numpy Parallel Behavior
- Our First Script
- Regarding Conda versus Anaconda
- The Second Script
- Types of Plots
QC¶
R¶
- Installing R Packages
- Publication-Quality Plots
- R Skills for Biological Data
- Session 3: R Data Wrangling
- Session 4: Publication-Quality Plots
- Session 7: R & Bioconductor on RCAC Clusters
- Single-Cell RNA-seq
REED Folder¶
RNA-seq¶
Scholar¶
- Accounts
- Apptainer
- Archive and compression
- Cancelling job
- Checking the job output
- Cluster Tools
- Collecting System Resource Utilization Data
- Compile gpu
- Compile hybrid
- Compile mpi
- Compile openmp
- Compile serial
- Compiling Source Code
- Creating the Submission Script
- Directives
- Environment variables
- FTP / SFTP
- File Storage and Transfer
- Files
- Frequently Asked Questions
- GPU Jobs
- Gateway (Open OnDemand)
- Generic SLURM Jobs
- Globus
- Holding a job
- Home directory
- Hsi
- Htar
- Interactive Apps
- Job dependencies
- Jobs
- Long term storage
- MPI Jobs
- Monitoring Resources
- Monitoring the Job
- Multiple Node Job
- OpenMP Jobs
- Python Example Jobs
- R Example Jobs
- Running Interactive Jobs on Scholar
- Running Jobs
- Running Serial Jobs
- Running Simple Jobs
- SCP
- Scholar Overview
- Scholar Spark Nodes
- Scholar User Guide
- Scratch space
- Sharing
- Slurm Queues and Partitions
- Software
- Storage quota
- Submitting the script as a job
- Tmp directory
- Windows network drive
Search¶
Slurm¶
- About Slurm Fairshare on RCAC clusters
- Gautschi's Universal Software Launcher
- Why is My Job Waiting? Decoding the Cluster Queue
Software¶
- Gautschi's Universal Software Launcher
- The "It Works on My Laptop" Dilemma: Managing Software with Modules
- Why is My Job Waiting? Decoding the Cluster Queue
Software Catalog¶
Tutorials¶
User Guide¶
VS Code¶
Visualization¶
- Advanced Plotting
- Animations
- Colormaps
- Envision Center
- Getting Started
- MatPlotLib Workshop Index Page
- Our First Script
- The Second Script
- Types of Plots