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Tufts TTS Research Technology Bioinformatics Workshops

Introduction to Tufts HPC Cluster

Tufts TTS Research Technology Bioinformatics Workshops

About
2022 Workshops
2022 Workshops
- Schedule
- Fall 2022
  Fall 2022
  - Intro to HPC/Slurm For Life Sciences
    Intro to HPC/Slurm For Life Sciences
    
    Introduction
    
    Cluster Account and Storage
    
    Login
    
    File Transfer
    
    Terninologies
    
    Compute Resources
    
    Software on the Cluster
    
    Tmux Session
    
    Interactive Session
    
    Job Status
    
    Intro To Linux
    
    Starting with Shell
    
    Bash Parameters
    
    Shell Navigation
    
    Creating & Manipulating Files
    
    Going Home
    
    Running an Interactive Session
    
    Example with BLAST
    
    BLAST Batch Script
  - Intro to RStudio For Life Sciences
    Intro to RStudio For Life Sciences
    
    Introduction
    
    Setup
    
    Intro To R Script
  - Intro To 16S Metabarcoding
    Intro To 16S Metabarcoding
    
    Introduction
    
    Background
    
    Setup
    
    Quality Control
    
    Error Model & ASVs
    
    Merging, Chimeras & Taxonomy
    
    Diversity Analysis
    
    Differential Abundance
  - Intro To Metagenomics
    Intro To Metagenomics
    
    Introduction
    
    Setup
    
    Workshop Notebook
  - Intro To Genome Technology
    Intro To Genome Technology
    
    Introduction
    
    Slides
  - Intro To AlphaFold2
    Intro To AlphaFold2
    
    Introduction
    
    Background
    
    Setup
    
    AlphaFold2 Algorithm
    
    AlphaFold2 Output
    
    PyMOL Visualization
    
    Optional: AlphaFold2 Batch Script
2023 Workshops
2023 Workshops
- Schedule
- Spring 2023
  Spring 2023
  - Finding & Analyzing Metagenomics Data
    Finding & Analyzing Metagenomics Data
    
    Introduction
    
    Searching For SRA Data
    
    STAT Taxonomic Analysis
    
    Kraken2 Taxonomic Analysis
    
    Compare STAT & Kraken2
  - RNA-Seq with Galaxy
    RNA-Seq with Galaxy
    
    Introduction
    
    Processing Raw Reads
    
    Read Alignment
    
    Gene Quantification
    
    Differential Expression
  - Cas12a Variant Structural Predictions With AlphaFold2
    Cas12a Variant Structural Predictions With AlphaFold2
    
    Introduction
    
    Introduction To Cas12a Variant Structural Predictions With AlphaFold2
    
    AlphaFold2 Accuracy Assessment
    
    Cas12a Variant Visualization
  - Trajectory Analysis
    Trajectory Analysis
    
    Introduction
    
    Setup and Monocle3 Objects
    
    Monocle3 Workflow and Trajectory Analysis
    
    Pseudotime and Differential Expression
2024 Workshops
2024 Workshops
- Schedule
- Spring 2024
  Spring 2024
  - Introduction to Metagenomics
    Introduction to Metagenomics
    
    In class hands-on session
    
    Take-home exercise
    
    Take-home exercise announcement
    
    Exercise Hint
    
    Example Report
  - Introduction to AlphaFold2
    Introduction to AlphaFold2
    
    Introduction
    
    Run AlphaFold2_CLI
    
    Run AlphaFold2 OpenOndemandApp
    
    Vizualize with PYMOL
    
    Slides
  - Running RNA-Seq analysis with nextflow & nf-core
    Running RNA-Seq analysis with nextflow & nf-core
    
    Introduction
    
    nf-core fetchngs
    
    nf-core rnaseq
    
    nf-core differentialabundance
    
    multiqc report
    
    differentialabundance report
- Fall 2024
  Fall 2024
  - Workshop Agenda
  - 1. Introduction to Tufts HPC Cluster
    1. Introduction to Tufts HPC Cluster
    
    Introduction to Tufts HPC Cluster Introduction to Tufts HPC Cluster
    Table of contents
    
    TTS - Research Technology
    
    Today's Topics
    
    Recording
    
    Tufts HPC Terminologies
    
    Getting to Know Tufts HPC Cluster Resources
    
    Tufts HPC Cluster Access
    
    Getting Work Done on Tufts HPC Cluster with SLURM
  - 2. Getting started with Bioinformatics on Tufts HPC
    2. Getting started with Bioinformatics on Tufts HPC
    
    Linux/Unix command line basics
    Linux/Unix command line basics
    
    Overview
    
    Introduction to Linux/Unix
    
    Files and File system
    
    Must-known Linux/Unix tools
    
    Conditional statements and loops
    
    Advanced Linux/Unix tools
    
    Available bioinformatics resources/tools on Tufts HPC
    
    How to run bioinformatics analysis on Tufts HPC
  - 3. Software installation and environment management in HPC
    3. Software installation and environment management in HPC
    
    Overview
    
    Application Installation from Source Codes
    
    R package Installation
    
    Conda Environment Management, Jupyer Kernel and Modules
    
    Simplying Conda Environment Management with conda-env-mod
  - 4. Advanced HPC workflows and job management
    4. Advanced HPC workflows and job management
    
    Overview
    
    Array jobs
    
    Nextflow Overview
    
    How to run nf-core pipelines

Introduction to Tufts HPC Cluster

Date: 10/09/2024

Delilah Maloney

Sr. HPC Specialist

TTS - Research Technology

Questions, Issues, Requests?

Contact us at: tts-research@tufts.edu

Research Technology Website

Today's Topics

Recording