From 25fd221043a6c1cd663152ce82cd3968805e3cd6 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Thu, 6 Apr 2023 15:36:00 -0400 Subject: [PATCH 1/5] start Teaching on AnVIL --- 01-instructor_guide.Rmd | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index d6753521..e6810f43 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -38,3 +38,11 @@ The `swirl` lessons touch on several additional R commands and concepts beyond t - [`dslabs`](https://cran.r-project.org/web/packages/dslabs/index.html) This book provides instructions on how to set these up in the cloud using the [AnVIL platform](https://anvil.terra.bio/), so that your students will not need to install anything. Depending on your needs, you might decide to run this activity on a different cloud provider, such [Posit Cloud](https://posit.cloud/) (formerly RStudio Cloud), or have your students install RStudio themselves. + +## Teaching on AnVIL + +The AnVIL (Analysis Visualization and Informatics Lab-space) platform is a cloud computing platform specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. + +AnVIl can be an excellent way to introduce students to biological data analysis and cloud computing. Because all computation on AnVIL is done in the cloud, all students can use the exact same computing environment through their browsers, with no need for software installation or access to expensive computers. + +If this is your first time using AnVIL (or first time using it for a course), the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide) provides a walkthrough of how to set up and teach a course or workshop on AnVIL. From f817df63d15b2aa1e6f1a8c79675afea546207b5 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 7 Apr 2023 14:52:52 -0400 Subject: [PATCH 2/5] add checklist and setup timeline --- 01-instructor_guide.Rmd | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index e6810f43..220e2594 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -46,3 +46,31 @@ The AnVIL (Analysis Visualization and Informatics Lab-space) platform is a cloud AnVIl can be an excellent way to introduce students to biological data analysis and cloud computing. Because all computation on AnVIL is done in the cloud, all students can use the exact same computing environment through their browsers, with no need for software installation or access to expensive computers. If this is your first time using AnVIL (or first time using it for a course), the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide) provides a walkthrough of how to set up and teach a course or workshop on AnVIL. + +### Checklist and Timeframe + +Here is a [checklist](https://docs.google.com/document/d/1-HqQqH_qlkHwRua8-b92MyKQcEmcl0Nk37rSYqP49aw/edit) to help you keep track of the steps for setting up and teaching on AnVIL. Details about each of these steps can be found in the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide). *Note that this checklist is written for workshop instructors as well as classroom instructors, so some of the "Event Setup" steps may not be applicable to you, depending on your teaching context.* + +Here is a suggested timeframe for working through the checklist: + +**1+ month before** + +- Figure out how you will fund the class/workshop +- Start working through INSTRUCTOR SETUP. It's a good idea to get billing figured out with plenty of time to spare +- Do any necessary EVENT SETUP steps + +**1+ week before** + +- Start working through RUNNING THE CLASS +- If possible, have students log in to AnVIL and send you their usernames, so you can add them to the Student Group ahead of time. This saves time on the day of the class. +- **Do not add students to your Billing Project** ahead of time. This prevents them from accruing costs. + +**Day of (or shortly before)** + +- Add students to Billing Project +- Have students clone the Workspace (They cannot do this until you have added them to the Billing Project. As soon as they do this, they can start computing.) + +**After** + +- Collect feedback, if you didn't do it during the class/workshop +- Work though EVENT WRAP-UP - until you shut things down, you will continue to accrue costs From e0c7fe3882bd6b2315543ac0f88ef1d729368dd0 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 7 Apr 2023 15:17:17 -0400 Subject: [PATCH 3/5] remove header numbering --- 01-instructor_guide.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 220e2594..da67e3ce 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -39,7 +39,7 @@ The `swirl` lessons touch on several additional R commands and concepts beyond t This book provides instructions on how to set these up in the cloud using the [AnVIL platform](https://anvil.terra.bio/), so that your students will not need to install anything. Depending on your needs, you might decide to run this activity on a different cloud provider, such [Posit Cloud](https://posit.cloud/) (formerly RStudio Cloud), or have your students install RStudio themselves. -## Teaching on AnVIL +## Teaching on AnVIL {-} The AnVIL (Analysis Visualization and Informatics Lab-space) platform is a cloud computing platform specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. @@ -47,7 +47,7 @@ AnVIl can be an excellent way to introduce students to biological data analysis If this is your first time using AnVIL (or first time using it for a course), the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide) provides a walkthrough of how to set up and teach a course or workshop on AnVIL. -### Checklist and Timeframe +### Checklist and Timeframe {-} Here is a [checklist](https://docs.google.com/document/d/1-HqQqH_qlkHwRua8-b92MyKQcEmcl0Nk37rSYqP49aw/edit) to help you keep track of the steps for setting up and teaching on AnVIL. Details about each of these steps can be found in the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide). *Note that this checklist is written for workshop instructors as well as classroom instructors, so some of the "Event Setup" steps may not be applicable to you, depending on your teaching context.* @@ -59,7 +59,7 @@ Here is a suggested timeframe for working through the checklist: - Start working through INSTRUCTOR SETUP. It's a good idea to get billing figured out with plenty of time to spare - Do any necessary EVENT SETUP steps -**1+ week before** +**~1 week before** - Start working through RUNNING THE CLASS - If possible, have students log in to AnVIL and send you their usernames, so you can add them to the Student Group ahead of time. This saves time on the day of the class. From 1dbe88a16041f14be18c9c03c5203a1171fbe750 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 7 Apr 2023 15:33:01 -0400 Subject: [PATCH 4/5] add bullet about preparing content --- 01-instructor_guide.Rmd | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index da67e3ce..d1aab8c4 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -56,7 +56,9 @@ Here is a suggested timeframe for working through the checklist: **1+ month before** - Figure out how you will fund the class/workshop -- Start working through INSTRUCTOR SETUP. It's a good idea to get billing figured out with plenty of time to spare +- Start working through INSTRUCTOR SETUP. + - It's a good idea to get billing figured out with plenty of time to spare + - Take some time to familiarize yourself with the content and make any desired updates or customizations. - Do any necessary EVENT SETUP steps **~1 week before** From 5383e7a9854343d5ac72cbee5ed5fe9bdaa47152 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 7 Apr 2023 15:41:25 -0400 Subject: [PATCH 5/5] add colons --- 01-instructor_guide.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index d1aab8c4..16bd6e6c 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -53,7 +53,7 @@ Here is a [checklist](https://docs.google.com/document/d/1-HqQqH_qlkHwRua8-b92My Here is a suggested timeframe for working through the checklist: -**1+ month before** +**1+ month before:** - Figure out how you will fund the class/workshop - Start working through INSTRUCTOR SETUP. @@ -61,18 +61,18 @@ Here is a suggested timeframe for working through the checklist: - Take some time to familiarize yourself with the content and make any desired updates or customizations. - Do any necessary EVENT SETUP steps -**~1 week before** +**~1 week before:** - Start working through RUNNING THE CLASS - If possible, have students log in to AnVIL and send you their usernames, so you can add them to the Student Group ahead of time. This saves time on the day of the class. - **Do not add students to your Billing Project** ahead of time. This prevents them from accruing costs. -**Day of (or shortly before)** +**Day of (or shortly before):** - Add students to Billing Project - Have students clone the Workspace (They cannot do this until you have added them to the Billing Project. As soon as they do this, they can start computing.) -**After** +**After:** - Collect feedback, if you didn't do it during the class/workshop - Work though EVENT WRAP-UP - until you shut things down, you will continue to accrue costs