July 16-20, 2018
Texas Advanced Computing Center
Learn the skills necessary to develop and execute life sciences workflows on large-scale computational systems. Run parallel analyses, use Bash and Python to chain common life sciences applications together to form more complex workflows, and leverage reproducibility techniquest to ensure your efforts are enduring. Spend time one-on-one with TACC’s Life Sciences Computing group discussing how to accelerate your existing research, or how to start a new project by beginning with the best computational practices.
Participants should bring their laptops and plan to participate actively. Laptops will require a terminal application for accessing compute resources.
AT&T wifi:
Coupon Code: WPiL-1T3C-1J
Instructors:
Click here for more information about the course instructors.
Etherpad
https://public.etherpad-mozilla.org/p/ctls2018
Agenda
Monday
| Time | Topic |
|---|---|
| 8:30 - 10:00 | Introduction to Computational Techniques for Life Science Research |
| 10:00 - 10:15 | Break |
| 10:15 - 11:45 | Introduction to High Performance Computing I: Introduction to Linux |
| 11:45 - 13:00 | Lunch and Small Group Discussions |
| 13:00 - 14:30 | Introduction to High Performance Computing II: Command Line Utilities |
| 14:30 - 14:45 | Break |
| 14:45 - 16:15 | Applied Hands-on Command Line - Examples for Life Sciences |
| 16:15 - 16:30 | Break |
| 16:30 - 17:00 | Daily Review and Hands-on Exercises |
Tuesday
| Time | Topic |
|---|---|
| 8:30 - 10:00 | HPC Software Environment |
| 10:00 - 10:15 | Break |
| 10:15 - 11:45 | Data Management and Collaboration Best Practices |
| 11:45 - 13:00 | Lunch |
| 13:00 - 14:30 | Choice of Intro to Python, Intro to RStudio, or Intermediate Bash |
| 14:30 - 14:45 | Break |
| 14:45 - 16:15 | Choice of Intermediate Python, Intermediate RStudio, or Advanced Bash |
| 16:15 - 16:30 | Break |
| 16:30 - 17:00 | Hands-on Exercises & Bring-your-own-code Workshop |
Wednesday
| Time | Topic |
|---|---|
| 8:30 - 10:00 | Developing Life Sciences Workflows Part 1 |
| 10:00 - 10:15 | Break |
| 10:15 - 11:45 | Developing Life Sciences Workflows Part 2 |
| 11:45 - 13:00 | Lunch |
| 13:00 - 14:30 | Optimization and Parallelization of Workflows for HPC Part 1 |
| 14:30 - 14:45 | Break |
| 14:45 - 16:00 | Optimization and Parallelization of Workflows for HPC Part 2 |
| 16:00 - 16:30 | Break |
| 16:30 - 17:00 | Hands-on Exercises & Bring-your-own-code Workshop |
Thursday
| Time | Topic |
|---|---|
| 8:30 - 10:00 | Best Practices for Reproducibility: Version Control |
| 10:00 - 10:15 | Break |
| 10:15 - 11:45 | Best Practices for Reproducibility in Research: Containers |
| 11:45 - 13:00 | Lunch |
| 13:00 - 14:30 | Best Practices for Reproducibility in Research: Reproducible Containers |
| 14:30 - 14:45 | Break |
| 14:45 - 16:15 | Best Practices for Reproducibility in Research: Reproducible Containers |
| 16:15 - 16:30 | Break |
| 16:30 - 17:00 | Daily Review and Hands-on Exercises |
Friday
| Time | Topic |
|---|---|
| 8:30 - 9:30 | Course Review and Next Steps |
| 9:30 - 11:45 | Bring your own code workshop / one-on-one assistance |
| 11:45 - 13:00 | Lunch |
| 13:00 - 17:00 | Bring your own code workshop / one-on-one assistance |