This box searches only this space. The box at the upper right searches the entire iPlant wiki.

Skip to end of metadata
Go to start of metadata


L:  Lecture

CA: Class Activity/Active Learning

DateLecture #TopicLearning OutcomesHomeworkSlides / ActivityAdditional Notes
8/27/20191(L) Intro to Course

Course introduction an dorientation

Importance of Cyberinfrastructure and Data Science

Homework 1- Intro and Data ScientistsLecture 1 Google Slides 
8/29/20192(CA) Working as a Team

Strengths and weaknesses of teams

Problems and solutions to common team problems

Homework 2 - Good enough practices

Team presentations

Discussion on teams

Teams give presentations on data scientists. Discussion on teams.
Software Carpentry
Bootcamp for anyone in command line and intro programmingLinux Command Line and Shell workshop  Optional for those wanting training/practice at the command line
9/3/20193(L) Good enough practices for data scienceData Science is a Team Activity
How to take care of code, project planning, etc.
Homework 3 - Best practicesLecture 3 Google Slides 
9/5/20194(CA) Take a big project and breaking it down

Overall project plan (and what it takes to plan a project)

Organization: Project Planning, Documentation, GitHub

Homework 3 - Best practicesLecture 4 Google Slides 
9/10/20195(L) Client Project: Wilson Leung (guest lecture)Mid-term project overviewHomework 4 - Client project setup

Slides (Wilson)

Lecture 5 Google Slides


Project Page for Midterm

Overview of breakdown projects: what do you need to deliver? How do you ensure everyone is on the same page for requirements.

 How will you utilize the resources to which you have access

Homework 5 - Client project concept maps and preliminary planLecture 6 Google Slides 
9/17/20197(L) What is the cloud and virtualizationCloud howto, introduction to Atmosphere, Chameleon , Jetstream Lecture 7 Google Slides 
9/19/20198(L) What is the cloud and virtualization (part 2)Hands on cloud and mapping things needed for Wilsons projectHomework 6 - Cloud costsLecture 7 Google SlidesNote – had additional discussion from previous lecture.
9/24/20199(CA) Hands on with the cloud and virtual machinesGetting comfortable with CLI and managing VM/installing s/w . Introduction to ContainersHomework 7 - Launching and Logging into a VM and command line tools Lecture 8 Google SlidesDue in class
9/26/201910(L) What are containers and how they different than virtual machines

What is virtualization, and the difference between VMs and Containers.

Homework 8 - Install SequenceServer on a VMLecture 9 - Virtualization and containers 
10/1/201911(L/CA) Hands on with containers

Differences between VMs and Containers (part II).

  • Hand's on (if there is time):
    • How to run a container
    • Modify a container
    • Create a docker file
    • Redistribute containers
Work on midtermLecture 10 - Virtualization and Containers Part II 

(CA) Hands on with containers

Backup: HPC Lecture

  • How to run a container

  • Modify a container

  • Create a docker file

  • Redistribute containers

Work on midtermLecture 11 - HPC TheoryAtmosphere may be down and interfere with in class Docker activities.
10/8/201913(CA) High performance computing

Intro to HPC and UA HPC

  • Logging into the system
  • How can I use the HPC?
  • Basics about the system and why it's good to know it
  • Useful commands on the HPC
  • How can I get help?
Work on midterm

Hands-on with containers


10/10/201914(CA) Hands on with HPC

How to log in and run applications on UA HPC

  • Docker -> Singularity
  • Using Singularity to access GPUs
Work on midtermUA HPC lecture: Blake Joyce 
10/15/201915(CA) Hands on with HPC/Singularity

Singularity is another container technology, but has additional security over Docker and user-level permissions (required for shared HPC resources)

Work on midtermHands-on 
10/17/201916(CA) Hands on with HPC and Benchmarking

Benchmarking is critical to scaling out analyses:

  • How long does an analysis take
  • What resources are required (CPUs, Memory, GPUs, etc.)
  • Where are there bottlenecks during scaling (e.g., multiple jobs reading/writing to a shared filesystem)
HPC homeworkSingularity and UA HPC Tutorial 
10/22/201917(L) Intro to workflow managers

What are workflow managers

Why are workflow managers needed

When to use a workflow manager


Homework - 9

Work on midterm

Recorded lecture

10/24/201918(CA) Hands on with workflowshands on exercises, run workflows on HPC, cloud, etc

Workflow homework

Note: Bonus homework (use your new-found distributed computing skills)

Recorded lecture

10/29/201919(L) Midterm updates and discussions

Midterm update

Theory to data management and data grids

Midterm progress reports

Work on midterm

Intro to data management theory

No slides 
10/31/201920(CA) Midterm presentationsHands-on with iRODS

Midterm progress reports

Hands-on with iRODS

CyVerse Data Store Quick Start Guide 
11/5/201921(CA)Midterm presentations    
11/7/201922(CA)Midterm presentations
11/12/201923(L)Final project/Special topics    
11/14/201924(CA)Final project/Special topics    
11/19/201925(L)Final project/Special topics    
11/21/201926(CA)Final project/Special topics    
11/26/201927(L)Final project/Special topics    
11/28/2019No Class     
12/3/201928(L)Final project/Special topics    
12/5/201929(CA)Final project/Special topics    
12/10/2019Last Class     
12/12/2019Reading Day     
Scheduled Final
8-10 AM in ECE 107 presentations, all term papers due  
12/19/2019All Work Due     


  • No labels