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GL4U: Amplicon Sequencing Bootcamp 2023 Pilot at CSULA
Welcome to the main page for the GeneLab for Colleges and Universities (GL4U) Amplicon Sequencing Bootcamp 2023 Pilot taking place at California State University, Los Angeles (CSULA)!
This course takes place Monday, 10-Jul-2023 to Thursday, 13-Jul-2023 in-person at CSULA 😊
The course utilizes lectures and hands-on coding in Jupyter Notebooks. It begins with the GL4U: Introduction Modules, which includes an overview of NASA Space Biology, NASA Open Life Sciences and the Open Science Data Repository (OSDR), GeneLab, and key foundational coding skills and concepts related to bioinformatics and working with sequencing data. Then it moves onto the GL4U: Amplicon Sequencing Modules, which provides an overview of amplicon sequencing and hands-on processing of samples derived from the Rodent Research - 6 mission, OSD-249, using the GeneLab Amplicon Sequencing Data Processing Pipeline followed by analysis and visualization of the processed data.
Lecture materials are linked in the schedule below, while Jupyter notebooks will be linked after the bootcamp.
Links to accessing the National Science Foundation (NSF) Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) cloud computers that will be used during the bootcamp can be found on this page.
Information on requesting ACCESS resources for teaching these bootcamp materials can be found on this page.
Information on how to set up an environment on a local computer capable of running the Jupyter notebooks can be found on this page.
The scheduled breaks for each day are:
- 11:30 am - 11:45 am
- 1:00 pm - 2:00 pm
NOTE
Lecture materials are linked in the schedule below, while Jupyter notebooks will be linked after the bootcamp.
| Time | Activity |
|---|---|
| 9:30 am - 10:00 am | Refreshments |
| 10:00 am - 11:30 am |
GL4U: Intro NASA Space Biology/OSDR/GeneLab Intro Lecture (pdf) |
| 11:30 am - 11:45 am | Break |
| 11:45 am - 1:00 pm |
GL4U: Intro NASA Space Biology/OSDR/GeneLab Intro Lecture continued (pdf) Short-read Sequencing Overview Lecture (pdf) |
| 1:00 pm - 2:00 pm | Lunch |
| 2:00 pm - 3:00 pm |
GL4U: Intro Short-read Sequencing Overview Lecture continued (pdf) |
| 3:00 pm - | Informal discussion |
| Time | Activity |
|---|---|
| 9:30 am - 10:00 am | Refreshments |
| 10:00 am - 11:30 am |
GL4U: Intro Command-Line, R, Jupyter Intro Lecture (pdf) Intro Notebooks |
| 11:30 am - 11:45 am | Break |
| 11:45 am - 1:00 pm |
GL4U: Intro Intro Notebooks continued |
| 1:00 pm - 2:00 pm | Lunch |
| 2:00 pm - 3:00 pm |
GL4U: Intro Intro Notebooks continued |
| 3:00 pm - | Informal discussion |
| Time | Activity |
|---|---|
| 9:30 am - 10:00 am | Refreshments |
| 10:00 am - 11:30 am |
GL4U: Intro Intro Notebooks continued GL4U: Amplicon Seq Amplicon Sequencing Overview Lecture (pdf) |
| 11:30 am - 11:45 am | Break |
| 11:45 am - 1:00 pm |
GL4U: Amplicon Seq Amplicon Sequencing Notebooks |
| 1:00 pm - 2:00 pm | Lunch |
| 2:00 pm - 3:00 pm |
GL4U: Amplicon Seq Amplicon Sequencing Notebooks continued |
| 3:00 pm - | Informal discussion |
| Time | Activity |
|---|---|
| 9:30 am - 10:00 am | Refreshments |
| 10:00 am - 11:30 am |
GL4U: Amplicon Seq Amplicon Sequencing Notebooks continued |
| 11:30 am - 11:45 am | Break |
| 11:45 am - 1:00 pm |
GL4U: Amplicon Seq Amplicon Sequencing Notebooks continued Amplicon Sequencing Processing and Analysis Appendix (pdf) --- JPL Planetary Protection Seminar |
| 1:00 pm - 2:00 pm |
Group Picture! Lunch |
| 2:00 pm - 3:00 pm | Complete the Post-Bootcamp Survey Discussion of utilizing ACCESS Cloud-computing Resources Individual computer setup |
| 3:00 pm - 3:30 pm | Closing remarks / Wrap-up |