From cc74098eb9d3057e7f0d13f99e040f256dc28500 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 29 Nov 2022 19:18:09 -0500 Subject: [PATCH 01/27] Create instructor_setup_AnVIL.Rmd --- instructor_setup_AnVIL.Rmd | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 instructor_setup_AnVIL.Rmd diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd new file mode 100644 index 00000000..2e37fbba --- /dev/null +++ b/instructor_setup_AnVIL.Rmd @@ -0,0 +1,27 @@ +# Setup on AnVIL + +## Workspace + +On AnVIL, all computing is done within "Workspaces". + +To make things easy for you and your students, we have created an AnVIL Workspace that contains all the files necessary for this exercise, which can be accessed at the following link: + + + +This is a public AnVIL Workspace, which is similar to "view only" mode for a document - you and your students can view it freely, but you will need to "clone" your own copy of it in order to do your own work (i.e. start up RStudio, Galaxy, or Jupyter Notebooks, or run a Workflow). + + +## Class Setup + +In order to make your own copy of the Workspace (so that you and your students can run RStudio), you must first set up Billing. + +There are two ways you can organize your class: + +**Option 1**: Instructor creates a single clone of the Workspace, and shares it with the whole class. + +This is simpler, particularly if you are new to AnVIL, but has some disadvantages: + + - With this setup, it is impossible to tell which students are running up compute costs - expenses are only reported for the class as a whole. + - Students will each get their own cloud environment (i.e. their own RStudio session), and some temporary storage space to go with it. But they will all share the same permanent storage, so if they need to save files, they may end up overwriting each others' files. + +This setup does have the advantage of being easier to shut down. Once your class is done, you can easily disable billing for the Workspace and prevent any further costs. From 7bf2d2f8f2ab6eb32e75eedb6d9efcc5ebd06b80 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 29 Nov 2022 19:19:52 -0500 Subject: [PATCH 02/27] Update _bookdown.yml --- _bookdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/_bookdown.yml b/_bookdown.yml index 186ff68c..59dfe493 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -3,6 +3,7 @@ chapter_name: "Chapter " repo: https://github.com/jhudsl/AnVIL_Template/ rmd_files: ["index.Rmd", "01-instructor_guide.Rmd", + "instructor_setup_AnVIL.Rmd", "02-student_instructions.Rmd", "03-exercises.Rmd", "exercises_swirl_01_04_05_06_12.Rmd", From 2659b7a1401e2845c87faf543a643885cde8788f Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 2 Dec 2022 14:10:25 -0500 Subject: [PATCH 03/27] add option students create workspace --- instructor_setup_AnVIL.Rmd | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 2e37fbba..b6c8b42f 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -17,7 +17,7 @@ In order to make your own copy of the Workspace (so that you and your students c There are two ways you can organize your class: -**Option 1**: Instructor creates a single clone of the Workspace, and shares it with the whole class. +**Option 1: Instructor creates a single clone of the Workspace, and shares it with the whole class.** This is simpler, particularly if you are new to AnVIL, but has some disadvantages: @@ -25,3 +25,13 @@ This is simpler, particularly if you are new to AnVIL, but has some disadvantage - Students will each get their own cloud environment (i.e. their own RStudio session), and some temporary storage space to go with it. But they will all share the same permanent storage, so if they need to save files, they may end up overwriting each others' files. This setup does have the advantage of being easier to shut down. Once your class is done, you can easily disable billing for the Workspace and prevent any further costs. + +**Option 2: Each student creates their own copy of the Workspace** + +This is a bit more work up to set up and to shut down, but is generally preferable for longer-term (i.e. multi-session) courses, especially if your students will need to save or share files. + + - Costs will be reported per student (i.e. per Workspace) + - Students will have their own permanent storage, and can't overwrite each other's files. + - This is essential for any activities in which they need to save and share a file, either to collaborate with peers or to submit for a grade. + - This is also necessary if they will be accessing files from multiple cloud environments (e.g. creating a file in Galaxy, then analyzing it in RStudio). + - This setup gives students more power (i.e. they are able to create additional Workspaces and invite others to use them, charging to your Billing Account). But it provides transparency about *who* is carrying out activities, enabling you to address any problems with individual students. From 1020b5d851e424c72f3a3780018b7f9ffb0fa78a Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 2 Dec 2022 14:17:30 -0500 Subject: [PATCH 04/27] remove statement that might be incorrect --- instructor_setup_AnVIL.Rmd | 2 -- 1 file changed, 2 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index b6c8b42f..c975dd74 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -24,8 +24,6 @@ This is simpler, particularly if you are new to AnVIL, but has some disadvantage - With this setup, it is impossible to tell which students are running up compute costs - expenses are only reported for the class as a whole. - Students will each get their own cloud environment (i.e. their own RStudio session), and some temporary storage space to go with it. But they will all share the same permanent storage, so if they need to save files, they may end up overwriting each others' files. -This setup does have the advantage of being easier to shut down. Once your class is done, you can easily disable billing for the Workspace and prevent any further costs. - **Option 2: Each student creates their own copy of the Workspace** This is a bit more work up to set up and to shut down, but is generally preferable for longer-term (i.e. multi-session) courses, especially if your students will need to save or share files. From 0328074254bd65cbce38a07a1c7bfd36d66e1269 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 5 Dec 2022 13:54:23 -0500 Subject: [PATCH 05/27] minor edits --- instructor_setup_AnVIL.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index c975dd74..e350d4ca 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -31,5 +31,5 @@ This is a bit more work up to set up and to shut down, but is generally preferab - Costs will be reported per student (i.e. per Workspace) - Students will have their own permanent storage, and can't overwrite each other's files. - This is essential for any activities in which they need to save and share a file, either to collaborate with peers or to submit for a grade. - - This is also necessary if they will be accessing files from multiple cloud environments (e.g. creating a file in Galaxy, then analyzing it in RStudio). - - This setup gives students more power (i.e. they are able to create additional Workspaces and invite others to use them, charging to your Billing Account). But it provides transparency about *who* is carrying out activities, enabling you to address any problems with individual students. + - This is also necessary if they will be passing files between different cloud environments (e.g. creating a file in Galaxy, then analyzing it in RStudio). + - This setup gives students more power (they are able to create additional Workspaces and invite others to use them, charging to your Billing Account). But it provides transparency about *who* is carrying out activities, enabling you to address any problems with individual students. From e6781536c35be48882f10f09f6fa328687a28350 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 6 Dec 2022 14:57:31 -0500 Subject: [PATCH 06/27] Update instructor_setup_AnVIL.Rmd --- instructor_setup_AnVIL.Rmd | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index e350d4ca..739bfe4e 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -1,5 +1,11 @@ # Setup on AnVIL +## Why use AnVIL in your classroom? + +## AnVIL Instructor guide + +If this is your first time using AnVIL (or first time using it for a course), we recommend checking out the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide). Several of the instructions below link out to the Instructor Guide for details. + ## Workspace On AnVIL, all computing is done within "Workspaces". @@ -13,9 +19,16 @@ This is a public AnVIL Workspace, which is similar to "view only" mode for a doc ## Class Setup -In order to make your own copy of the Workspace (so that you and your students can run RStudio), you must first set up Billing. +In order to make your own copy of the Workspace (so that you and your students can run RStudio), you must first: + +1. **Set up Billing** to fund your students' activities. + a. [Set up a Google Account](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) (AnVIL is powered by Google Cloud behind the scenes). + b. [Create a Google Billing Account]() (this is how Google charges you for your students' activities). + c. [Create Terra Billing Project(s)]() (this is how you manage students and give them permission to compute on AnVIL). +3. **Collect usernames**: You will need to know the usernames that your students will be using to access AnVIL. +4. **Set up Groups**: [Creating "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. -There are two ways you can organize your class: +Once you have set up Billing and Groups, there are two ways you can organize your class and give students access to the material: **Option 1: Instructor creates a single clone of the Workspace, and shares it with the whole class.** From 50b224eb3066ea3eab97fe057bc01cf7ccbd666d Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 6 Dec 2022 19:33:42 -0500 Subject: [PATCH 07/27] reorder instructor setup --- instructor_setup_AnVIL.Rmd | 33 ++++++++++++++++++++------------- 1 file changed, 20 insertions(+), 13 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 739bfe4e..7cdf868e 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -6,20 +6,10 @@ If this is your first time using AnVIL (or first time using it for a course), we recommend checking out the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide). Several of the instructions below link out to the Instructor Guide for details. -## Workspace - -On AnVIL, all computing is done within "Workspaces". - -To make things easy for you and your students, we have created an AnVIL Workspace that contains all the files necessary for this exercise, which can be accessed at the following link: - - - -This is a public AnVIL Workspace, which is similar to "view only" mode for a document - you and your students can view it freely, but you will need to "clone" your own copy of it in order to do your own work (i.e. start up RStudio, Galaxy, or Jupyter Notebooks, or run a Workflow). - ## Class Setup -In order to make your own copy of the Workspace (so that you and your students can run RStudio), you must first: +In order for your students to be able to compute on AnVIL, you must first: 1. **Set up Billing** to fund your students' activities. a. [Set up a Google Account](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) (AnVIL is powered by Google Cloud behind the scenes). @@ -28,16 +18,33 @@ In order to make your own copy of the Workspace (so that you and your students c 3. **Collect usernames**: You will need to know the usernames that your students will be using to access AnVIL. 4. **Set up Groups**: [Creating "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. + +## Workspace + +On AnVIL, all computing is done within "Workspaces". + +To make things easy for you and your students, we have created an AnVIL Workspace that contains all the files necessary for this exercise, which can be accessed at the following link: + + + +This is a public AnVIL Workspace, which is similar to "view only" mode for a document - you and your students can view it freely, but you will need to "clone" your own copy of it in order to do your own work (i.e. start up RStudio, Galaxy, or Jupyter Notebooks, or run a Workflow). + +## Clone Workspace + Once you have set up Billing and Groups, there are two ways you can organize your class and give students access to the material: -**Option 1: Instructor creates a single clone of the Workspace, and shares it with the whole class.** +### Option 1: Instructor clones + +**Instructor creates a single clone of the Workspace, and shares it with the whole class.** This is simpler, particularly if you are new to AnVIL, but has some disadvantages: - With this setup, it is impossible to tell which students are running up compute costs - expenses are only reported for the class as a whole. - Students will each get their own cloud environment (i.e. their own RStudio session), and some temporary storage space to go with it. But they will all share the same permanent storage, so if they need to save files, they may end up overwriting each others' files. -**Option 2: Each student creates their own copy of the Workspace** +### Option 2: Students clone + +**Each student creates their own copy of the Workspace** This is a bit more work up to set up and to shut down, but is generally preferable for longer-term (i.e. multi-session) courses, especially if your students will need to save or share files. From 5232604a908771abdc7587c9b6442b80b0412f16 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 6 Dec 2022 19:49:26 -0500 Subject: [PATCH 08/27] some work on instructor setup --- instructor_setup_AnVIL.Rmd | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 7cdf868e..aaa2c838 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -29,9 +29,7 @@ To make things easy for you and your students, we have created an AnVIL Workspac This is a public AnVIL Workspace, which is similar to "view only" mode for a document - you and your students can view it freely, but you will need to "clone" your own copy of it in order to do your own work (i.e. start up RStudio, Galaxy, or Jupyter Notebooks, or run a Workflow). -## Clone Workspace - -Once you have set up Billing and Groups, there are two ways you can organize your class and give students access to the material: +There are two ways you can organize your class and give students access to the material: ### Option 1: Instructor clones @@ -46,10 +44,16 @@ This is simpler, particularly if you are new to AnVIL, but has some disadvantage **Each student creates their own copy of the Workspace** -This is a bit more work up to set up and to shut down, but is generally preferable for longer-term (i.e. multi-session) courses, especially if your students will need to save or share files. +This is a bit more work up to set up, but is generally preferable for longer-term (i.e. multi-session) courses, especially if your students will need to save or share files. - Costs will be reported per student (i.e. per Workspace) - Students will have their own permanent storage, and can't overwrite each other's files. - This is essential for any activities in which they need to save and share a file, either to collaborate with peers or to submit for a grade. - This is also necessary if they will be passing files between different cloud environments (e.g. creating a file in Galaxy, then analyzing it in RStudio). - This setup gives students more power (they are able to create additional Workspaces and invite others to use them, charging to your Billing Account). But it provides transparency about *who* is carrying out activities, enabling you to address any problems with individual students. + +:::{.warning} + +If you are new to AnVIL, you will need to request a "Project Quota Increase". In order to prevent abuse, Google has limits that restrict the number of Workspaces that can be created by new accounts (as of Dec 2022, new users are limited to 5 Workspaces). + +::: From 3761ffece6ce1eb9c1915551792e521731de27d1 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Thu, 8 Dec 2022 14:30:12 -0500 Subject: [PATCH 09/27] add "What is AnVIL?" --- instructor_setup_AnVIL.Rmd | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index aaa2c838..6ebdd063 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -1,5 +1,19 @@ # Setup on AnVIL +## What is AnVIL? + +The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https://anvilproject.org/) is a cloud computing platform specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. + + + +:::{.notice} +**AnVIL in a nutshell** + +- Behind the scenes, AnVIL relies on Google Cloud Platform to provide computing infrastructure. Basically, AnVIL lets you "rent" computers from Google (remotely). Whenever you run an analyses on AnVIL, it actually runs on one of Google's computers, and AnVIL lets you see the results in your browser. +- AnVIL uses [Terra](https://anvil.terra.bio/) to provide many computational tools useful for biological data analysis, such as [RStudio](https://www.rstudio.com/products/rstudio/), [Galaxy](https://usegalaxy.org/), and [Jupyter Notebooks](https://jupyter.org/). Terra takes care of installing these tools on Google's computers, so that you can just start using them. +- AnVIL and Terra provide their services for free (managing software, data, and users). You just need to pay Google for the computational resources that you use. +::: + ## Why use AnVIL in your classroom? ## AnVIL Instructor guide @@ -12,11 +26,11 @@ If this is your first time using AnVIL (or first time using it for a course), we In order for your students to be able to compute on AnVIL, you must first: 1. **Set up Billing** to fund your students' activities. - a. [Set up a Google Account](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) (AnVIL is powered by Google Cloud behind the scenes). - b. [Create a Google Billing Account]() (this is how Google charges you for your students' activities). - c. [Create Terra Billing Project(s)]() (this is how you manage students and give them permission to compute on AnVIL). + a. [Set up a Google Account](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) - AnVIL is powered by Google Cloud behind the scenes. + b. (Some users) [Set up Google Billing Account]() - This is how Google charges you for your students' activities. Depending on how you are being funded, this may be taken care of for you. If your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), contact them to determine whether you need to do any Billing administration through Google. + c. [Create Terra Billing Project(s)]() - This is how you manage students and give them permission to compute on AnVIL. 3. **Collect usernames**: You will need to know the usernames that your students will be using to access AnVIL. -4. **Set up Groups**: [Creating "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. +4. **Set up Groups**: [Creating Terra "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. ## Workspace From 59563b95dfb4a473ad4629329d2ce55612a74683 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Thu, 8 Dec 2022 14:59:36 -0500 Subject: [PATCH 10/27] fix youtube link --- instructor_setup_AnVIL.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 6ebdd063..ba346018 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -4,7 +4,7 @@ The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https://anvilproject.org/) is a cloud computing platform specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. - + :::{.notice} **AnVIL in a nutshell** From d99d314b3bd63a060139c5b11db6e2fe84b1e275 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Thu, 8 Dec 2022 15:02:23 -0500 Subject: [PATCH 11/27] break up big paragraph --- instructor_setup_AnVIL.Rmd | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index ba346018..f32d922f 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -26,8 +26,9 @@ If this is your first time using AnVIL (or first time using it for a course), we In order for your students to be able to compute on AnVIL, you must first: 1. **Set up Billing** to fund your students' activities. - a. [Set up a Google Account](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) - AnVIL is powered by Google Cloud behind the scenes. - b. (Some users) [Set up Google Billing Account]() - This is how Google charges you for your students' activities. Depending on how you are being funded, this may be taken care of for you. If your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), contact them to determine whether you need to do any Billing administration through Google. + a. [Set up a Google Account](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) - You need a Google account to access AnVIL + b. (Some users) [Set up Google Billing Account]() - This is how Google charges you for your students' activities. + - Depending on how you are being funded, this may be taken care of for you. If your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), contact them to determine whether you need to do any billing administration through Google. c. [Create Terra Billing Project(s)]() - This is how you manage students and give them permission to compute on AnVIL. 3. **Collect usernames**: You will need to know the usernames that your students will be using to access AnVIL. 4. **Set up Groups**: [Creating Terra "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. From c7ebee8ae7451a5c563bb433d5c77c0c96693999 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:07:25 -0500 Subject: [PATCH 12/27] first draft of timeline table --- instructor_setup_AnVIL.Rmd | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index f32d922f..971be3ad 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -1,5 +1,29 @@ # Setup on AnVIL +## Suggested Timeline + + +```{r, echo=FALSE} +timeline <- tibble::tribble( + ~When, ~What, + + "2+ weeks before", paste( + "- **Set up billing**", + " - If you're handling the billing yourself, this can be done in < 1 hr with a credit card. + " - But if your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), it may take a little while to get everything set up. + "- **Add TAs and coinstructors**", + "- **Run through material** - make sure you're able to" + " - Clone the Workspace" + " - Start up RStudio, load swirl, and start the first lesson" + " - Load the dataset for the project," + " - Use `dplyr` commands, such as `dplyr::filter()` + sep="\n"), + "~1 week before", "**Collect student usernames** so you can grant them access", + "Day of", "" +) +knitr::kable(timeline, format = "html") +``` + ## What is AnVIL? The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https://anvilproject.org/) is a cloud computing platform specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. @@ -23,6 +47,10 @@ If this is your first time using AnVIL (or first time using it for a course), we ## Class Setup +:::{.notice} +**Tip**: It's helpful to have your students sign into AnVIL and provide you with their username ahead of time, so that you can grant permissions to them before the class begins. +::: + In order for your students to be able to compute on AnVIL, you must first: 1. **Set up Billing** to fund your students' activities. From 1892c328fbdc235073dba08b13d0797335807fdf Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:12:52 -0500 Subject: [PATCH 13/27] fix timeline table --- instructor_setup_AnVIL.Rmd | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 971be3ad..41b93e4b 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -9,14 +9,15 @@ timeline <- tibble::tribble( "2+ weeks before", paste( "- **Set up billing**", - " - If you're handling the billing yourself, this can be done in < 1 hr with a credit card. - " - But if your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), it may take a little while to get everything set up. + " - If you're handling the billing yourself, this can be done in < 1 hr with a credit card.", + " - But if your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), it may take a little while to get everything set up.", + "- **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", "- **Add TAs and coinstructors**", - "- **Run through material** - make sure you're able to" - " - Clone the Workspace" - " - Start up RStudio, load swirl, and start the first lesson" - " - Load the dataset for the project," - " - Use `dplyr` commands, such as `dplyr::filter()` + "- **Run through material** - make sure you're able to", + " - Clone the Workspace", + " - Start up RStudio, load swirl, and start the first lesson", + " - Load the dataset for the project", + " - Use `dplyr` commands, such as `dplyr::filter()`", sep="\n"), "~1 week before", "**Collect student usernames** so you can grant them access", "Day of", "" From d0864f75d06655787c1ccad119dab30ddd9c7427 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:22:07 -0500 Subject: [PATCH 14/27] edit timeline table --- instructor_setup_AnVIL.Rmd | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 41b93e4b..70b38c18 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -8,9 +8,8 @@ timeline <- tibble::tribble( ~When, ~What, "2+ weeks before", paste( - "- **Set up billing**", - " - If you're handling the billing yourself, this can be done in < 1 hr with a credit card.", - " - But if your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), it may take a little while to get everything set up.", + "- **Set up billing**, + "- **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class "- **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", "- **Add TAs and coinstructors**", "- **Run through material** - make sure you're able to", From 60f9a889e40197792e02f66efec910441a349ad4 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:23:30 -0500 Subject: [PATCH 15/27] remove column names from table --- instructor_setup_AnVIL.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 70b38c18..c558c44d 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -21,7 +21,7 @@ timeline <- tibble::tribble( "~1 week before", "**Collect student usernames** so you can grant them access", "Day of", "" ) -knitr::kable(timeline, format = "html") +knitr::kable(timeline, col.names = NULL, format = "html") ``` ## What is AnVIL? From 3b59f4bf35cbb0df5dcc1ac2a5253d59050067a3 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:28:32 -0500 Subject: [PATCH 16/27] edit timeline table --- instructor_setup_AnVIL.Rmd | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index c558c44d..9ece02ba 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -18,7 +18,10 @@ timeline <- tibble::tribble( " - Load the dataset for the project", " - Use `dplyr` commands, such as `dplyr::filter()`", sep="\n"), - "~1 week before", "**Collect student usernames** so you can grant them access", + "~1 week before", paste( + "- **Collect student usernames**", + "- **Add students to class group**, + sep="\n"), "Day of", "" ) knitr::kable(timeline, col.names = NULL, format = "html") From c285266505c7311ce8618ed5a5d7d395ee243d5c Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:29:11 -0500 Subject: [PATCH 17/27] edit timeline table --- instructor_setup_AnVIL.Rmd | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 9ece02ba..9da43178 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -21,8 +21,7 @@ timeline <- tibble::tribble( "~1 week before", paste( "- **Collect student usernames**", "- **Add students to class group**, - sep="\n"), - "Day of", "" + sep="\n") ) knitr::kable(timeline, col.names = NULL, format = "html") ``` From 294b0b261e69cc13aef62ba3123a51c95b4e0124 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:30:35 -0500 Subject: [PATCH 18/27] fix table --- instructor_setup_AnVIL.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 9da43178..25dcd319 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -8,7 +8,7 @@ timeline <- tibble::tribble( ~When, ~What, "2+ weeks before", paste( - "- **Set up billing**, + "- **Set up billing**", "- **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class "- **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", "- **Add TAs and coinstructors**", From 30859f8b83a3b52650ea6c45c1a359972a2da210 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 14:34:53 -0500 Subject: [PATCH 19/27] fix timeline table --- instructor_setup_AnVIL.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 25dcd319..d160b3c0 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -9,7 +9,7 @@ timeline <- tibble::tribble( "2+ weeks before", paste( "- **Set up billing**", - "- **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class + "- **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class", "- **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", "- **Add TAs and coinstructors**", "- **Run through material** - make sure you're able to", From d00c39b1a02337642c01bb2bde358dfd1bbe42e1 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 15:11:14 -0500 Subject: [PATCH 20/27] fix timeline table --- instructor_setup_AnVIL.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index d160b3c0..e176fc53 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -20,7 +20,7 @@ timeline <- tibble::tribble( sep="\n"), "~1 week before", paste( "- **Collect student usernames**", - "- **Add students to class group**, + "- **Add students to class group**", sep="\n") ) knitr::kable(timeline, col.names = NULL, format = "html") From f28eb69b704258a855c6864ccb34846fcae5c5c9 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 9 Dec 2022 15:23:23 -0500 Subject: [PATCH 21/27] timeline table formatting --- instructor_setup_AnVIL.Rmd | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index e176fc53..b080b9aa 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -7,20 +7,20 @@ timeline <- tibble::tribble( ~When, ~What, - "2+ weeks before", paste( - "- **Set up billing**", - "- **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class", - "- **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", - "- **Add TAs and coinstructors**", - "- **Run through material** - make sure you're able to", + "**2+ weeks before**", paste( + "1. **Set up billing**", + "1. **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class", + "1. **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", + "1. **Add TAs and coinstructors**", + "1. **Run through material** - make sure you're able to", " - Clone the Workspace", " - Start up RStudio, load swirl, and start the first lesson", " - Load the dataset for the project", " - Use `dplyr` commands, such as `dplyr::filter()`", sep="\n"), - "~1 week before", paste( - "- **Collect student usernames**", - "- **Add students to class group**", + "**~1 week before**", paste( + "1. **Collect student usernames**", + "1. **Add students to class group**", sep="\n") ) knitr::kable(timeline, col.names = NULL, format = "html") From cd6032920816b1436a5fdc0f3e553be55721df2e Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 12 Dec 2022 14:41:43 -0500 Subject: [PATCH 22/27] reorganize and try fixing timeline table --- instructor_setup_AnVIL.Rmd | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index b080b9aa..c8a924b7 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -1,5 +1,9 @@ # Setup on AnVIL +## AnVIL Instructor guide + +If this is your first time using AnVIL (or first time using it for a course), we recommend checking out the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide). Several of the instructions below link out to the Instructor Guide for details. + ## Suggested Timeline @@ -19,14 +23,14 @@ timeline <- tibble::tribble( " - Use `dplyr` commands, such as `dplyr::filter()`", sep="\n"), "**~1 week before**", paste( - "1. **Collect student usernames**", - "1. **Add students to class group**", + "1. **Set up billing**", + "1. **Set up billing**", sep="\n") ) knitr::kable(timeline, col.names = NULL, format = "html") ``` -## What is AnVIL? +## About AnVIL The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https://anvilproject.org/) is a cloud computing platform specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. @@ -40,12 +44,7 @@ The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https:// - AnVIL and Terra provide their services for free (managing software, data, and users). You just need to pay Google for the computational resources that you use. ::: -## Why use AnVIL in your classroom? - -## AnVIL Instructor guide - -If this is your first time using AnVIL (or first time using it for a course), we recommend checking out the [AnVIL Instructor Guide](https://jhudatascience.org/AnVIL_Book_Instructor_Guide). Several of the instructions below link out to the Instructor Guide for details. - +### Why use AnVIL in your classroom? ## Class Setup From 71ef6df58429cb86d64cafe72db24f8436b2d78a Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 12 Dec 2022 14:42:32 -0500 Subject: [PATCH 23/27] remove AnVIL in a nutshell div --- instructor_setup_AnVIL.Rmd | 2 -- 1 file changed, 2 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index c8a924b7..4c4f6184 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -36,13 +36,11 @@ The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https:// -:::{.notice} **AnVIL in a nutshell** - Behind the scenes, AnVIL relies on Google Cloud Platform to provide computing infrastructure. Basically, AnVIL lets you "rent" computers from Google (remotely). Whenever you run an analyses on AnVIL, it actually runs on one of Google's computers, and AnVIL lets you see the results in your browser. - AnVIL uses [Terra](https://anvil.terra.bio/) to provide many computational tools useful for biological data analysis, such as [RStudio](https://www.rstudio.com/products/rstudio/), [Galaxy](https://usegalaxy.org/), and [Jupyter Notebooks](https://jupyter.org/). Terra takes care of installing these tools on Google's computers, so that you can just start using them. - AnVIL and Terra provide their services for free (managing software, data, and users). You just need to pay Google for the computational resources that you use. -::: ### Why use AnVIL in your classroom? From e0e669237cae865e9eeb08212b2bcef34f76a3e5 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 12 Dec 2022 14:43:40 -0500 Subject: [PATCH 24/27] remove "AnVIL in a nutshell" title --- instructor_setup_AnVIL.Rmd | 2 -- 1 file changed, 2 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 4c4f6184..f023b38f 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -36,8 +36,6 @@ The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https:// -**AnVIL in a nutshell** - - Behind the scenes, AnVIL relies on Google Cloud Platform to provide computing infrastructure. Basically, AnVIL lets you "rent" computers from Google (remotely). Whenever you run an analyses on AnVIL, it actually runs on one of Google's computers, and AnVIL lets you see the results in your browser. - AnVIL uses [Terra](https://anvil.terra.bio/) to provide many computational tools useful for biological data analysis, such as [RStudio](https://www.rstudio.com/products/rstudio/), [Galaxy](https://usegalaxy.org/), and [Jupyter Notebooks](https://jupyter.org/). Terra takes care of installing these tools on Google's computers, so that you can just start using them. - AnVIL and Terra provide their services for free (managing software, data, and users). You just need to pay Google for the computational resources that you use. From 1755f00543da2e5772d349958d219275cf281027 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 12 Dec 2022 14:54:29 -0500 Subject: [PATCH 25/27] trying to fix timeline table --- instructor_setup_AnVIL.Rmd | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index f023b38f..2245a0ee 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -22,10 +22,17 @@ timeline <- tibble::tribble( " - Load the dataset for the project", " - Use `dplyr` commands, such as `dplyr::filter()`", sep="\n"), - "**~1 week before**", paste( - "1. **Set up billing**", + "**2+ weeks before**", paste( "1. **Set up billing**", - sep="\n") + "1. **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class", + "1. **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", + "1. **Add TAs and coinstructors**", + "1. **Run through material** - make sure you're able to", + " - Clone the Workspace", + " - Start up RStudio, load swirl, and start the first lesson", + " - Load the dataset for the project", + " - Use `dplyr` commands, such as `dplyr::filter()`", + sep="\n"), ) knitr::kable(timeline, col.names = NULL, format = "html") ``` From 802517e460bfd90981779e3e09b6d007d7382e22 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 12 Dec 2022 15:14:27 -0500 Subject: [PATCH 26/27] give up on timeline table --- instructor_setup_AnVIL.Rmd | 52 ++++++++++++++------------------------ 1 file changed, 19 insertions(+), 33 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index 2245a0ee..c9e65693 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -6,36 +6,26 @@ If this is your first time using AnVIL (or first time using it for a course), we ## Suggested Timeline +### 2+ weeks before + +1. [**Set up a Google Account**](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) - You need a Google account to access AnVIL] +1. **Set up billing** + a. (Some users) [Set up Google Billing Account]() - Depending on how you are being funded, this may be taken care of for you. If your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), contact them to determine whether you need to do any billing administration through Google. + b. [Create Terra Billing Project(s)]() - This is how you manage students and give them permission to compute on AnVIL. +3. **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class +4. **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance. +5. **Add TAs and coinstructors** +6. **Run through material** - make sure you're able to + - Clone the Workspace + - Start up RStudio, load swirl, and start the first lesson + - Load the dataset for the project + - Use `dplyr` commands, such as `dplyr::filter()` + +### 1 week before + +1. **Collect student usernames** - have students log in to AnVIL +1. **Add students to class group** -```{r, echo=FALSE} -timeline <- tibble::tribble( - ~When, ~What, - - "**2+ weeks before**", paste( - "1. **Set up billing**", - "1. **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class", - "1. **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", - "1. **Add TAs and coinstructors**", - "1. **Run through material** - make sure you're able to", - " - Clone the Workspace", - " - Start up RStudio, load swirl, and start the first lesson", - " - Load the dataset for the project", - " - Use `dplyr` commands, such as `dplyr::filter()`", - sep="\n"), - "**2+ weeks before**", paste( - "1. **Set up billing**", - "1. **Request Quota Increase** so that you have permission to create enough Workspaces for your whole class", - "1. **Notify Terra** of the date(s) of your class, so they can ensure AnVIL is not down for maintenance.", - "1. **Add TAs and coinstructors**", - "1. **Run through material** - make sure you're able to", - " - Clone the Workspace", - " - Start up RStudio, load swirl, and start the first lesson", - " - Load the dataset for the project", - " - Use `dplyr` commands, such as `dplyr::filter()`", - sep="\n"), -) -knitr::kable(timeline, col.names = NULL, format = "html") -``` ## About AnVIL @@ -58,10 +48,6 @@ The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https:// In order for your students to be able to compute on AnVIL, you must first: 1. **Set up Billing** to fund your students' activities. - a. [Set up a Google Account](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) - You need a Google account to access AnVIL - b. (Some users) [Set up Google Billing Account]() - This is how Google charges you for your students' activities. - - Depending on how you are being funded, this may be taken care of for you. If your funding is being managed by a third party (e.g. through a funding mechanism such as [STRIDES](https://datascience.nih.gov/strides), or through your institution), contact them to determine whether you need to do any billing administration through Google. - c. [Create Terra Billing Project(s)]() - This is how you manage students and give them permission to compute on AnVIL. 3. **Collect usernames**: You will need to know the usernames that your students will be using to access AnVIL. 4. **Set up Groups**: [Creating Terra "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. From 3470edda4f818e2a9072194eebec1159ab5b0b66 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 12 Dec 2022 15:20:11 -0500 Subject: [PATCH 27/27] remove numbering on timeline sections --- instructor_setup_AnVIL.Rmd | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/instructor_setup_AnVIL.Rmd b/instructor_setup_AnVIL.Rmd index c9e65693..68455ec7 100644 --- a/instructor_setup_AnVIL.Rmd +++ b/instructor_setup_AnVIL.Rmd @@ -6,7 +6,7 @@ If this is your first time using AnVIL (or first time using it for a course), we ## Suggested Timeline -### 2+ weeks before +### 2+ weeks before {-} 1. [**Set up a Google Account**](https://jhudatascience.org/AnVIL_Book_Instructor_Guide/creating-an-instructor-account.html) - You need a Google account to access AnVIL] 1. **Set up billing** @@ -21,11 +21,10 @@ If this is your first time using AnVIL (or first time using it for a course), we - Load the dataset for the project - Use `dplyr` commands, such as `dplyr::filter()` -### 1 week before - -1. **Collect student usernames** - have students log in to AnVIL -1. **Add students to class group** +### 1 week before {-} +1. **Collect student usernames** - have students log in to AnVIL and then provide you with their username +1. **Set up Groups**: [Creating Terra "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. ## About AnVIL @@ -45,11 +44,6 @@ The [AnVIL (Analysis Visualization and Informatics Lab-space) platform](https:// **Tip**: It's helpful to have your students sign into AnVIL and provide you with their username ahead of time, so that you can grant permissions to them before the class begins. ::: -In order for your students to be able to compute on AnVIL, you must first: - -1. **Set up Billing** to fund your students' activities. -3. **Collect usernames**: You will need to know the usernames that your students will be using to access AnVIL. -4. **Set up Groups**: [Creating Terra "Groups"]() makes it much easier manage your students and TAs/co-instructors on AnVIL. ## Workspace