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GL4U: RNAseq Virtual Bootcamp 2024
Welcome to the main page for the GeneLab for Colleges and Universities (GL4U) RNA Sequencing (RNAseq) Virtual Bootcamp 2024!
This course will be held virtually via Microsoft Teams over two consecutive weekends:
Friday, 27-Sept-2024 to Sunday, 29-Sept-2024, and Friday, 04-Oct-2024 to Saturday, 05-Oct-2024
The course utilizes lectures and hands-on coding in Jupyter Notebooks (JNs). 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: RNAseq Modules, which provides an overview of RNA sequencing and hands-on processing of samples derived from the Rodent Research - 1 mission, OSD-104, using the GeneLab RNA Sequencing Data Processing Pipeline followed by analysis and visualization of the processed data.
Lecture materials and JNs are linked in the schedule below (coming soon).
- Day 1: Friday, 27-Sept-2024
- Day 2: Saturday, 28-Sept-2024
- Day 3: Sunday, 29-Sept-2024
- Day 4: Friday, 04-Oct-2024
- Day 5: Saturday, 05-Oct-2024
Create a GitHub account (if you don't already have one):
- During the bootcamp we will be using GitPod, which offers free monthly compute resources using your GitHub account.
- If you don't already have an account, go to https://github.com/join to create one before the start of the bootcamp.
Prerequisites:
- This bootcamp is designed to be accessible to participants with little to no coding experience.
Although, some prior coding experience will be helpful.
- Completion of high-school biology is required.
Some college-level course work in molecular biology will help make the material easier to digest.
GL4U: Introduction Modules
- To run the 4 GL4U Intro JNs listed in the schedule below, follow the instructions on the GL4U_Intro_2024 GitHub branch.
NOTE: The links in the schedule below are only to the JNs. These JNs are not able to be run unless they are accessed through GitPod as instructed in the GL4U_Intro_2024 GitHub branch README.md.
GL4U: RNAseq Modules
- To run the 2 GL4U RNAseq JNs listed in the schedule below, follow the instructions on the GL4U_RNAseq_2024 GitHub branch.
NOTE: The links in the schedule below are only to the JNs. These JNs are not able to be run unless they are accessed through GitPod as instructed in the GL4U_RNAseq_2024 GitHub branch README.md.
The scheduled bootcamp times, including breaks, for each day are:
Bootcamp times:
8am - 3pm PDT | 9am - 4pm MDT | 10am - 5pm CDT
- Morning break: 930am - 945am PDT | 1030am - 1045am MDT | 1130am - 1145am CDT
- Lunch break: 11am - noon PDT | noon - 1pm MDT | 1pm - 2pm CDT
- Afternoon break: 130pm - 145pm PDT | 230pm - 245pm MDT | 330pm - 345pm CDT
NOTE: Lecture materials and JNs are linked below.
| Time | Activity | Video Recording |
|---|---|---|
| 8am - 815am PDT 9am - 915am MDT 10am - 1015am CDT |
Introduction | |
| 815am - 930am PDT 915am - 1030am MDT 1015am - 1130am CDT |
GL4U: Intro NASA, SMD, Space Biology Overview Lecture OSDR and GeneLab Overview Lecture |
GL4U: Intro NASA, SMD, Space Biology Overview Lecture Recording OSDR and GeneLab Overview Lecture Recording |
| 930am - 945am PDT 1030am - 1045am MDT 1130am - 1145am CDT |
BREAK | |
| 945am - 11am PDT 1045am - noon MDT 1145am - 1pm CDT |
GL4U: Intro OSDR and GeneLab Overview Lecture Command-Line, R, Jupyter Intro Lecture |
GL4U: Intro OSDR and GeneLab Overview Lecture Recording Command-Line, R, Jupyter Intro Lecture Recording |
| 11am - noon PDT noon - 1pm MDT 1pm - 2pm CDT |
LUNCH | |
| noon - 130pm PDT 1pm - 230pm MDT 2pm - 330pm CDT |
GL4U: Intro Jupyter Intro JN Unix Intro JN |
|
| 130pm - 145pm PDT 230pm - 245pm MDT 330pm - 345pm CDT |
BREAK | |
| 145pm - 3pm PDT 245pm - 4pm MDT 345pm - 5pm CDT |
GL4U: Intro Unix Intro JN |
| Time | Activity | Video Recording |
|---|---|---|
| 8am - 815am PDT 9am - 915am MDT 10am - 1015am CDT |
Questions from Day 1 | |
| 815am - 930am PDT 915am - 1030am MDT 1015am - 1130am CDT |
GL4U: Intro Unix Intro JN |
|
| 930am - 945am PDT 1030am - 1045am MDT 1130am - 1145am CDT |
BREAK | |
| 945am - 11am PDT 1045am - noon MDT 1145am - 1pm CDT |
GL4U: Intro R Intro JN |
|
| 11am - noon PDT noon - 1pm MDT 1pm - 2pm CDT |
LUNCH | |
| noon - 130pm PDT 1pm - 230pm MDT 2pm - 330pm CDT |
GL4U: Intro R Intro JN |
|
| 130pm - 145pm PDT 230pm - 245pm MDT 330pm - 345pm CDT |
BREAK | |
| 145pm - 3pm PDT 245pm - 4pm MDT 345pm - 5pm CDT |
GL4U: Intro R Intro JN Short Read Sequencing Overview Lecture |
GL4U: Intro Short Read Sequencing Overview Lecture Recording |
| Time | Activity | Video Recording |
|---|---|---|
| 8am - 815am PDT 9am - 915am MDT 10am - 1015am CDT |
Questions from Day 2 | |
| 815am - 930am PDT 915am - 1030am MDT 1015am - 1130am CDT |
GL4U: Intro Short Read Sequencing Overview Lecture |
GL4U: Intro Short Read Sequencing Overview Lecture Recording |
| 930am - 945am PDT 1030am - 1045am MDT 1130am - 1145am CDT |
BREAK | |
| 945am - 11am PDT 1045am - noon MDT 1145am - 1pm CDT |
GL4U: Intro Short Read Sequencing Overview Lecture Sequencing data QC JN |
GL4U: Intro Short Read Sequencing Overview Lecture Recording |
| 11am - noon PDT noon - 1pm MDT 1pm - 2pm CDT |
LUNCH | |
| noon - 130pm PDT 1pm - 230pm MDT 2pm - 330pm CDT |
GL4U: RNAseq RNAseq Overview Lecture |
GL4U: RNAseq RNAseq Overview Lecture Recording, part 1 of 3 |
| 130pm - 145pm PDT 230pm - 245pm MDT 330pm - 345pm CDT |
BREAK | |
| 145pm - 3pm PDT 245pm - 4pm MDT 345pm - 5pm CDT |
GL4U: RNAseq RNAseq Overview Lecture RNAseq Processing JN |
GL4U: RNAseq RNAseq Overview Lecture Recording, part 1 of 3 |
| Time | Activity | Video Recording |
|---|---|---|
| 8am - 815am PDT 9am - 915am MDT 10am - 1015am CDT |
Questions from Days 1-3 | |
| 815am - 930am PDT 915am - 1030am MDT 1015am - 1130am CDT |
GL4U: RNAseq RNAseq Processing JN |
|
| 930am - 945am PDT 1030am - 1045am MDT 1130am - 1145am CDT |
BREAK | |
| 945am - 11am PDT 1045am - noon MDT 1145am - 1pm CDT |
GL4U: RNAseq RNAseq Processing JN RNAseq Overview Lecture |
GL4U: RNAseq RNAseq Overview Lecture Recording, part 2 of 3 |
| 11am - noon PDT noon - 1pm MDT 1pm - 2pm CDT |
LUNCH | |
| noon - 130pm PDT 1pm - 230pm MDT 2pm - 330pm CDT |
GL4U: RNAseq RNAseq Overview Lecture |
GL4U: RNAseq RNAseq Overview Lecture Recording, part 2 of 3 |
| 130pm - 145pm PDT 230pm - 245pm MDT 330pm - 345pm CDT |
BREAK | |
| 145pm - 3pm PDT 245pm - 4pm MDT 345pm - 5pm CDT |
GL4U: RNAseq RNAseq Overview Lecture RNAseq Processing JN |
GL4U: RNAseq RNAseq Overview Lecture Recording, part 2 of 3 |
| HOMEWORK |
GL4U: RNAseq Statistics Intro Lecture |
GL4U: RNAseq Statistics Overview Lecture Recording |
| Time | Activity | Video Recording |
|---|---|---|
| 8am - 815am PDT 9am - 915am MDT 10am - 1015am CDT |
Questions from Day 4 | |
| 815am - 930am PDT 915am - 1030am MDT 1015am - 1130am CDT |
GL4U: RNAseq RNAseq Overview Lecture RNAseq Processing JN |
GL4U: RNAseq RNAseq Overview Lecture Recording, part 3 of 3 |
| 930am - 945am PDT 1030am - 1045am MDT 1130am - 1145am CDT |
BREAK | |
| 945am - 11am PDT 1045am - noon MDT 1145am - 1pm CDT |
GL4U: RNAseq RNAseq Analysis JN |
|
| 11am - noon PDT noon - 1pm MDT 1pm - 2pm CDT |
LUNCH | |
| noon - 130pm PDT 1pm - 230pm MDT 2pm - 330pm CDT |
GL4U: RNAseq RNAseq Analysis JN |
|
| 130pm - 145pm PDT 230pm - 245pm MDT 330pm - 345pm CDT |
BREAK | |
| 145pm - 3pm PDT 245pm - 4pm MDT 345pm - 5pm CDT |
GL4U: RNAseq RNAseq Analysis JN Bootcamp Wrap-Up Post-Bootcamp Survey Closing Remarks |
IMPORTANT: Do NOT complete the post-bootcamp survey until you have completed ALL lectures and ALL hands on activities (JNs) for BOTH the GL4U: Introduction module set and the GL4U: RNAseq module set.
Send an e-mail to Amanda ([email protected]) verifying that you have completed all of the GL4U: Introduction content, all of the GL4U: RNAseq content listed below, and that you have completed the post-bootcamp survey:
Note: If you missed any one of the live sessions covering the content below, you will have to watch the recordings of the lectures you missed and complete the Jupyter Notebooks (JNs) that you missed. Each lecture recording is linked to in the schedule above.
GL4U: Introduction Certificate of Completion
-
GL4U: Intro Lectures:
-
- 01-jupyter-intro.ipynb
- 02-unix-intro.ipynb
- 03-R-intro.ipynb
- 04-sequencing-data-QC.ipynb
GL4U: RNAseq Certificate of Completion
-
GL4U: RNAseq Lectures:
- RNA Sequencing (RNAseq) Overview
- Statistics Overview
-
- 01-RNAseq_processing.ipynb
- 02-RNAseq_analysis.ipynb
GL4U Post-Bootcamp Survey
AFTER you have successfully completed all of BOTH the GL4U: Intro content and the GL4U: RNAseq content listed above (either live or on your own by watching the recordings and completing the hands-on JNs), click on this link and complete the post-bootcamp survey.