-
-### Video examples
-
-To show videos in your course, you can use markdown syntax like this:
-
-[A video we want to show](https://www.youtube.com/embed/VOCYL-FNbr0)
-
-Alternatively, you can use `knitr::include_url()` like this:
-Note that we are using `echo=FALSE` in the code chunk because we don't want the code part of this to show up.
-If you are unfamiliar with [how R Markdown code chunks work, read this](https://rmarkdown.rstudio.com/lesson-3.html).
-
-```{r, echo=FALSE}
-knitr::include_url("https://www.youtube.com/embed/VOCYL-FNbr0")
-```
-
-OR this works:
-
-
-
-### Links to files
-
-This works:
-
-```{r, fig.align="center", echo=FALSE}
-knitr::include_url("https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf", height = "800px")
-```
-
-Or this:
-
-[This works](https://genetics-gsa.org/education/genetics-learning-framework/).
-
-Or this:
-
-
-
-### Links to websites
-
-Examples of including a website link.
-
-This works:
-
-```{r, fig.align="center", echo=FALSE}
-knitr::include_url("https://yihui.org")
-```
-
-OR this:
-
-
-
-OR this:
-
-
-
-### Citation examples
-
-We can put citations at the end of a sentence like this [@rmarkdown2021].
-Or multiple citations [@rmarkdown2021, @Xie2018].
-
-but they need a ; separator [@rmarkdown2021; @Xie2018].
-
-In text, we can put citations like this @rmarkdown2021.
-
-### Callout boxes
-
-There are some preset callout boxes available, which can be used like so:
-
-`notice`:
-
-::: {.notice}
-Here's something interesting.
-:::
-
-`warning`:
-
-::: {.warning}
-Look out!
-:::
-
-`dictionary`:
-
-::: {.dictionary}
-Here's a definition.
-:::
-
-`reflection`:
-
-::: {.reflection}
-Consider this!
-:::
-
-`github`:
-
-::: {.github}
-Here's how you use GitHub.
-:::
-
-`wip`:
-
-::: {.wip}
-This section is a **Work in Progress**.
-:::
-
-### Dropdown summaries
-
-
+
+
+Once you are in proper billing project, you click on "View detailed charges" in the Billing section on the far right.
+
+
+
+
+
+This takes you to a report of the detailed charges accrued by the billing account. Here, you will be able to see the total cost over a time range, as well as costs broken down by services.
+
+
+
+
+
+# Setting up the Class Activity
+
+## Overview of Class Setup
+
+This section will show you how to organize your class to make it easier to administer access to your content. You will need to have a list of who will be taking your class, such as a course roster or sign-up list, as well as a list of additional instructors or teaching assistants. You can make changes later, so the list of students need not be final.
+
+## Collect Google IDs
+
+AnVIL IDs are based on [Google accounts](account-setup.html#google-account).
+
+Students -- Contact students/participants to get their AnVIL IDs. These should be Gmail addresses or emails with GSuite capabilities. You can link students to [Student Account Setup](student-account-setup.html) for instructions on what they should do.
+
+Co-instructors -- If you will be working with other instructors, such as co-instructors or teaching assistants, you will need to collect their IDs as well.
+
+## Set Up Groups
+Reminder:
+
+- Google **Billing Accounts** are managed on Google Cloud Platform and are used for organizing *funding sources* (e.g. credit cards, cloud credits).
+- Terra **Billing Projects** are managed through Terra, and allow you to associate your Terra activity with the correct Google Billing Account.
+
+For a more detailed explanation, please see the chapter on Account Setup.
+
+We suggest creating two different Terra Billing Projects under the appropriate Billing Account that you created on `cloud.google.com`: one for students and one for co-instructors. The instructions below will walk you through how to set this up.
+
+Groups enable you to share your class Workspace and manage permissions for many people at once. We recommend starting with one Group for instructors and one Group for students.
+
+### Instructor Group {#instructor-group} {-}
+
+Create an informative, unique Group name for any co-instructors and teaching assistants. We suggest a combination of institution-class-role (e.g., “jhu-bmr2021-instructors”). Only letters, numbers, underscores, and dashes are allowed in Group names. To create a Group for instructors:
+
+1. Go to https://anvil.terra.bio/#groups
+
+1. Click “+ Create a New Group”
+
+ ```{r, echo=FALSE, fig.alt='Screenshot of the Terra Group page. The "Create a New Group" button is highlighted.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag/edit#slide=id.gdb96a00840_0_6")
+ ```
+
+1. Type in your instructor Group name
+
+1. Click “CREATE GROUP”
+
+ ```{r, echo=FALSE, fig.alt='Screenshot of the Terra Group page with Create New Group pop out box. The Group name, jhu-bmr2021-instructors, has been entered and the "CREATE GROUP" button is highlighted.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag/edit#slide=id.gdb96a00840_0_16")
+ ```
+
+You now have a unique **instructor Group**.
+
+#### Add Instructors as "Admin" (Instructor Group) {-}
+
+Now that your instructor Group has been created, you should add any additional instructors. You should also ensure that they have the correct permissions.
+
+1. Go to https://anvil.terra.bio/#groups/ and click on the instructor Group name. This page should also be visible at `https://anvil.terra.bio/#groups/- -## Video overview on using Jupyter Notebooks - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_jupyter_video.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Launching Jupyter - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_jupyter_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Video overview on using Galaxy - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_video.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Starting Galaxy - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_start.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Navigating Galaxy - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_navigate.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Deleting Galaxy - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_galaxy_delete.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Video overview on using RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_video.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Launching RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Touring RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_tour.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Pausing RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_pause.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Deleting RStudio - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_rstudio_delete.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Pausing vs. Deleting cloud environments - -These instructions can be customized to a specific cloud environment by setting `AnVIL_module_settings$cloud_environment` before running `cow::borrow_chapter()`. If these variables have not been set, it defaults to "your cloud environment". - -### Generic cloud environment - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_cloud_environment_pause_vs_delete.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -### RStudio - -``` -AnVIL_module_settings <- list(cloud_environment = "RStudio") -cow::borrow_chapter( - doc_path = "child/_child_cloud_environment_pause_vs_delete.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -AnVIL_module_settings <- list(cloud_environment = "RStudio") - -cow::borrow_chapter( - doc_path = "child/_child_cloud_environment_pause_vs_delete.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: diff --git a/08-student_guide.Rmd b/08-student_guide.Rmd new file mode 100644 index 0000000..9e0f414 --- /dev/null +++ b/08-student_guide.Rmd @@ -0,0 +1,169 @@ +# (PART\*) Student Guide to AnVIL {-} + + +```{r, include = FALSE} +ottrpal::set_knitr_image_path() +``` + +# Using RStudio on AnVIL + +In the next few steps, you will walk through how to get set up to use RStudio on the AnVIL platform. AnVIL is centered around different “Workspaces”. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment. + +Use a web browser to go to the AnVIL website. In the browser type: + +``` +anvil.terra.bio +``` + +:::{.notice} +**Tip** +At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other. +::: + +Your instructor will give you information on which workspace you should clone. + +## Video overview of RStudio on AnVIL + +```{r, echo = FALSE, results='asis'} +cow::borrow_chapter( + doc_path = "child/_child_rstudio_video.Rmd", + repo_name = "jhudsl/AnVIL_Template" +) +``` + +## Launching RStudio + +```{r, echo = FALSE, results='asis'} +cow::borrow_chapter( + doc_path = "child/_child_rstudio_launch.Rmd", + repo_name = "jhudsl/AnVIL_Template" +) +``` + +## Touring RStudio + +```{r, echo = FALSE, results='asis'} +cow::borrow_chapter( + doc_path = "child/_child_rstudio_tour.Rmd", + repo_name = "jhudsl/AnVIL_Template" +) +``` + +## Pausing RStudio + +```{r, echo = FALSE, results='asis'} +cow::borrow_chapter( + doc_path = "child/_child_rstudio_pause.Rmd", + repo_name = "jhudsl/AnVIL_Template" +) +``` + + +# Using Galaxy on AnVIL + +In the next few steps, you will walk through how to get set up to use Galaxy on the AnVIL platform. AnVIL is centered around different “Workspaces”. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment. + +Use a web browser to go to the AnVIL website. In the browser type: + +``` +anvil.terra.bio +``` + +:::{.notice} +**Tip** +At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other. +::: + +Your instructor will give you information on which workspace you should clone. After logging in, click “View Workspaces”. Select the “Public” tab. In the top search bar type the activity workspace. + +Clone the workspace by clicking the teardrop button ({#id .class width=25 height=20px}). And selecting “Clone”. + +```{r, echo=FALSE, fig.alt='Screenshot showing the teardrop button. The button has been clicked revealing the "clone" option. The Clone option and the teardrop button are highlighted.'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_625") +``` + +In the first box, give your Workspace clone a name by adding an underscore (“_”) and your name. For example, “SARS-CoV-2-Genome_Ava_Hoffman”. Next, select the Billing project provided by your instructor. Leave the bottom two boxes as-is and click “CLONE WORKSPACE”. + +```{r, echo=FALSE, fig.alt='Screenshot showing the "clone a workspace" popout. The Workspace name, Billing Project, and Clone Workspace button have been filled in and highlighted.'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_648") +``` + +## Video overview on using Galaxy + +```{r, echo = FALSE, results='asis'} +cow::borrow_chapter( + doc_path = "child/_child_galaxy_video.Rmd", + repo_name = "jhudsl/AnVIL_Template" +) +``` + + +## Starting Galaxy {#starting-galaxy} + +Galaxy is a free, relatively easy to use bioinformatics implementation package. It changes command line programs into GUI based programs and is a great tool for performing bioinformatics analysis without having to update software or worry too much about coding. In order to use Galaxy, we need to create a cloud environment. This is like quickly renting a few computers from Google as the engine to power our Galaxy analysis. + +:::{.warning} +Currently, you will need to use Chrome or Safari as your browser for Galaxy cloud environments to work. +::: + +In your new Workspace, click on the “ANALYSES” tab. Next, click on “START”. You should see a popup window on the right side of the screen. Click on the Galaxy logo to proceed. + +```{r, echo=FALSE, fig.alt='Screenshot of the Workspace Notebooks tab. The notebook tab name and the plus button that starts a cloud environment for Galaxy have been highlighted,'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_788") +``` + +Click on “NEXT” and “CREATE” to keep all settings as-is. + +```{r, echo=FALSE, fig.alt='The CREATE button among cloud environments has been highlighted.'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_798") +``` + +Click on the Galaxy icon. + +```{r, echo=FALSE, fig.alt='The Galaxy icon appears if the environment has been successfully launched.'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.g2283b458fae_100_31") +``` + +You will see that the environment is still being set up. + +```{r, echo=FALSE, fig.alt='The status of the cloud computing environment shows that it is still being set up.'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.g2283b458fae_100_38") +``` + +This will take 8-10 minutes. When it is done, click “Open”. You might need to refresh the page. + +```{r, echo=FALSE, fig.alt='The Provisioning status text has changed to "Launch Galaxy" indicating the cloud environment is ready to use.'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.g2283b458fae_100_46") +``` + +:::{.notice} +Remember that you can refresh your browser or navigate away at any time. This is because the connection to the environment is in the cloud, not on your personal computer. +::: + +You can also follow along with the first ~2 minutes of [this video](https://jhudatascience.org/AnVIL_Book_Getting_Started/starting-galaxy.html) to start Galaxy on AnVIL. + +## Navigating Galaxy + +Notice the three main sections. + +**Tools** - These are all of the bioinformatics tool packages available for you to use. + +**The Main Dashboard** - This contains flash messages and posts when you first open Galaxy, but when we are using data this is the main interface area. + +**History** - When you start a project you will be able to see all of the documents in the project in the history. Now be aware, this can become very busy. Also the naming that Galaxy uses is not very intuitive, so you must make sure that you label your files with something that makes sense to you. + +```{r, echo=FALSE, fig.alt='Screenshot of the Galaxy landing page. The Tools and History headings have been highlighted.'} +ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_816") +``` + +On the welcome page, there are links to tutorials. You may try these out on your own. If you want to try a new analysis this is a good place to start. + +## Deleting Galaxy + +```{r, echo = FALSE, results='asis'} +cow::borrow_chapter( + doc_path = "child/_child_galaxy_delete.Rmd", + repo_name = "jhudsl/AnVIL_Template" +) +``` + diff --git a/08-student_modules.Rmd b/08-student_modules.Rmd deleted file mode 100644 index efb5178..0000000 --- a/08-student_modules.Rmd +++ /dev/null @@ -1,141 +0,0 @@ -```{r echo = FALSE} -knitr::opts_chunk$set(out.width = "100%") -``` - -# Student instructions - -Modules aimed at students in a course or workshop. - -
- -## Student Account Setup - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_student_create_account.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Student instructions for cloning a Workspace - -These instructions can be customized to a specific workspace by setting certain variables before running `cow::borrow_chapter()`. If these variables have not been set, reasonable defaults are provided (e.g. "ask your instructor"). - -### With no variables set: - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_student_workspace_clone.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -### With variables set: - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -# Specify variables -AnVIL_module_settings <- list( - workspace_name = "Example_Workspace", - workspace_link = "http://example.com/", - billing_project = "Example Billing Project" -) - -cow::borrow_chapter( - doc_path = "child/_child_student_workspace_clone.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Student instructions for launching Jupyter - -The module below is specially customized for students, allowing you to give more specific instructions on the settings for their Jupyter environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing Jupyter, Deleting Jupyter) that can be found in other chapters of this book. - -The following instructions can be customized by setting certain variables before running `cow::borrow_chapter()`. Developers should create these variables as a list `AnVIL_module_settings`. The following variables can be provided: - -- `audience` = Defaults to `general`, telling them to use the default Jupyter settings. If `audience` is set to `student`, it gives more specific instructions. -- `docker_image` = Optional, it will tell them how to set the image. -- `startup_script` = Optional, it will tell them how to set the script. - -### Using default Jupyter environment: - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -# Specify variables -AnVIL_module_settings <- list( - audience = "student" -) - -cow::borrow_chapter( - doc_path = "child/_child_jupyter_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -### Using custom Jupyter environment: - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -# Specify variables -AnVIL_module_settings <- list( - audience = "student", - docker_image = "example docker", - startup_script = "example startup script" -) - -cow::borrow_chapter( - doc_path = "child/_child_jupyter_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Student instructions for launching RStudio - -The module below is specially customized for students, allowing you to give more specific instructions on the settings for their RStudio environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing RStudio, Deleting RStudio) that can be found in other chapters of this book. - -The following instructions can be customized by setting certain variables before running `cow::borrow_chapter()`. Developers should create these variables as a list `AnVIL_module_settings`. The following variables can be provided: - -- `audience` = Defaults to `general`, telling them to use the default RStudio settings. If `audience` is set to `student`, it gives more specific instructions. -- `docker_image` = Optional, it will tell them to open the customization dialogue and direct them on how to set the image. -- `startup_script` = Optional, it will tell them to open the customization dialogue and direct them on how to set the script. - -### Using default RStudio environment: - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -# Specify variables -AnVIL_module_settings <- list( - audience = "student" -) - -cow::borrow_chapter( - doc_path = "child/_child_rstudio_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -### Using custom RStudio environment: - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -# Specify variables -AnVIL_module_settings <- list( - audience = "student", - docker_image = "example docker", - startup_script = "example startup script" -) - -cow::borrow_chapter( - doc_path = "child/_child_rstudio_launch.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: diff --git a/09-antismash_module.Rmd b/09-antismash_module.Rmd new file mode 100644 index 0000000..44b26e2 --- /dev/null +++ b/09-antismash_module.Rmd @@ -0,0 +1,35 @@ +```{r, include = FALSE} +ottrpal::set_knitr_image_path() +``` + +# Exploring Biosynthetic Gene Clusters + +In this module, you will examine the chicken gut microbiome samples for evidence of selection on biosynthetic gene clusters. + +## Background + +*Secondary metabolites* are organic compounds produced by a living organism that are _not_ directly used for normal growth, development, or reproduction. Secondary metabolites are sometimes called specialized metabolites, and these compounds play roles in how the organisms interacts with the environment. They may aid in protecting against stressors that are either biotic (e.g., the presence of other microbes competing for the same resources, which may produce toxic compounds against competitors) or abiotic (e.g., heavy metals in the soil, high external salt concentrations, or particularly acidic or alkaline soil). + +These metabolites are produced by a group of genes known as *biosynthetic gene clusters* (BGCs). Genes within a BGC are physically close to each other and also encode a biosynthetic pathway that produces a secondary metabolite [Medema et al. 2015](https://www.nature.com/articles/nchembio.1890) + +BGCs produce compounds with a huge range of applications, including pharmaceuticals, natural toxins (and toxin degradation), and molecules for chemical communication or chemical warfare between organisms. BGCs are also important for getting nutrients, vitamin biosynthesis, and *antimicrobial resistance*. We will focus on this last part during the exercise. + +## Before You Start + +```{r, echo = FALSE, results='asis'} +cow::borrow_chapter( + doc_path = "child/_child_google_create_account.Rmd", + repo_name = "jhudsl/AnVIL_Template" +) +``` + +## Objectives + +This activity will teach you how to: +1. Import annotated data into a Galaxy environment +1. Detect BGCs and predict NRPS and PKS metabolite structures for annotated bacterial or fungal genomes + + + + + diff --git a/09-student_guide.Rmd b/09-student_guide.Rmd deleted file mode 100644 index d6fff4a..0000000 --- a/09-student_guide.Rmd +++ /dev/null @@ -1,10 +0,0 @@ - -# Student Guide - -## Activity One - -You might want to create a student guide that contains a different subset of Rmd files from your book, or renders to a different output format (e.g. word document). You can specify the output and Rmd files that will be used for the student guide using the `_output.yml` and `_bookdown.yml` files in the student-guide directory. - -## Activity Two - -Steps of the guide could go here. \ No newline at end of file diff --git a/10-user_management_modules.Rmd b/10-user_management_modules.Rmd deleted file mode 100644 index e618f21..0000000 --- a/10-user_management_modules.Rmd +++ /dev/null @@ -1,38 +0,0 @@ -# User Management - -Modules about Groups and user management - -
- -## Create Terra Group - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_terra_group_create.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Add Member to Terra Group - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_terra_group_add_member.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: - -## Find Group Email - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_terra_group_find_email.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: diff --git a/11-why-anvil.Rmd b/11-why-anvil.Rmd deleted file mode 100644 index c8d7e59..0000000 --- a/11-why-anvil.Rmd +++ /dev/null @@ -1,16 +0,0 @@ -# Why AnVIL - -Modules describing why AnVIL is useful for different personas. - -
- -## Why AnVIL for Instructors? - -:::: {.borrowed_chunk} -```{r, echo = FALSE, results='asis'} -cow::borrow_chapter( - doc_path = "child/_child_why_AnVIL_instructor.Rmd", - repo_name = "jhudsl/AnVIL_Template" -) -``` -:::: diff --git a/GDSCN_BioDIGS_AMR.Rproj b/GDSCN_BioDIGS_AMR.Rproj new file mode 100644 index 0000000..21a4da0 --- /dev/null +++ b/GDSCN_BioDIGS_AMR.Rproj @@ -0,0 +1,17 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source diff --git a/_bookdown.yml b/_bookdown.yml index bae5ce5..1f9e90b 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -1,18 +1,15 @@ -book_filename: "Course_Name" +book_filename: "BioDIGS in the Classroom: Antimicrobial Resistance" chapter_name: "Chapter " -repo: https://github.com/jhudsl/AnVIL_Template/ +repo: https://github.com/fhdsl/GDSCN_BioDIGS_AMR/ rmd_files: ["index.Rmd", - "01-intro.Rmd", - "02-chapter_of_course.Rmd", - "03-AnVIL_modules.Rmd", - "04-workspace_modules.Rmd", - "05-billing_modules.Rmd", - "06-onboarding_modules.Rmd", - "07-using_platforms_modules.Rmd", - "08-student_modules.Rmd", - "10-user_management_modules.Rmd", - "11-why-anvil.Rmd", - "12-instructor_modules.Rmd", + "01-BioDIGS_project_overview.Rmd", + "02-research_team.Rmd", + "03-data_tour.Rmd", + "04-billing_modules.Rmd", + "05-anvil_onboarding.Rmd", + "06-using_galaxy.Rmd", + "08-student_guide.Rmd", + "07-instructor_guide.Rmd", "About.Rmd", "References.Rmd"] new_session: yes diff --git a/_output.yml b/_output.yml index f1d6e6a..ff151c4 100644 --- a/_output.yml +++ b/_output.yml @@ -1,21 +1,20 @@ bookdown::gitbook: # When using multiple css files, the default file path will be the first one # - css: [assets/style.css, assets/AnVIL_style/anvil.css] + css: [assets/style.css, assets/GDSCN_style/gdscn.css] includes: - in_header: GA_Script.html - before_body: assets/AnVIL_style/big-image_anvil.html - after_body: assets/AnVIL_style/footer.html + before_body: assets/GDSCN_style/big-image_gdscn.html + after_body: assets/GDSCN_style/footer.html highlight: tango config: toc: collapse: section before: | -
+ 
after: |
-
+
-# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows. You can deactivate this behavior in config_automation.yml.
\ No newline at end of file
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/book.bib b/book.bib
index ec95aa4..aed6138 100644
--- a/book.bib
+++ b/book.bib
@@ -1,3 +1,75 @@
+@article{BrevikBurgess2014,
+ author = {Eric C Brevik and Lynn C Burgess},
+ title = {The Influence of Soils on Human Health},
+ journal = {Nature Education Knowledge},
+ year = {2014},
+ url = {https://www.nature.com/scitable/knowledge/library/the-influence-of-soils-on-human-health-127878980/}
+}
+
+@article{Buffalari2020,
+ author = {Deanne Buffalari and Joyce J Fernandes and Leah Chase and Barbara Lom and Matthew S McMurray and Mary E Morrison and Amy Jo Stavnezer},
+ title = {Integrating Research into the Undergraduate Curriculum: 1. Early Research Experiences and Training},
+ journal = {Journal of Undergraduate Neuroscience Education},
+ year = {2020},
+ url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040836/}
+}
+
+@article{Canner2017,
+ author = {Judith E Canner and Archana J McEligot and María-Eglée Pérez and Lei Qian and Xinzhi Zhang},
+ title = {Enhancing Diversity in Biomedical Data Science},
+ journal = {Ethnicity & Disease},
+ year = {2017},
+ url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398168/}
+}
+
+@article{GDSCN2022,
+ author = {GDSCN},
+ title = {Diversifying the genomic data science research community},
+ journal = {Genome Research},
+ year = {2022},
+ url = {https://doi.org/10.1101/gr.276496.121}
+}
+
+@article{Gorovtsov2018,
+ author = {Andrey Vladimirovich Gorovtsov and Ivan Sergeevich Sazykin and Marina Alexandrovna Sazykina},
+ title = {The influence of heavy metals, polyaromatic hydrocarbons, and polychlorinated biphenyls pollution on the development of antibiotic resistance in soils},
+ journal = {Environmental Science and Pollution Research},
+ year = {2018},
+ url = {https://doi.org/10.1007/s11356-018-1465-9}
+}
+
+@article{Jones2022,
+ author = {Daleniece Higgins Jones and Xinhua Yu and Qian Guo and Xiaoli Duan and Chunrong Jia},
+ title = {Racial Disparities in the Heavy Metal Contamination of Urban Soil in the Southeastern United States},
+ journal = {International Journal of Environmental Research and Public Health},
+ year = {2022},
+ url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8834334/}
+}
+
+@article{Jurkowski2017,
+ author = {Anne Jurkowski and Ann H Reid and Jay B Labov},
+ title = {Metagenomics: A Call for Bringing a New Science into the Classroom (While It's Still New)},
+ journal = {CBE - Life Sciences Education},
+ year = {2017},
+ url = {https://doi.org/10.1187/cbe.07-09-0075}
+}
+
+@article{Khan2023,
+ author = {Muhammad Amjad Khan and Javed Nawab and Anwarzeb Khan and Mark L Brusseau and Shah Nawaz Khan and Neelum Ali and Saraj Bahadur and Sardar Khan and Qing Huang},
+ title = {Human Health and Ecological Risks Associated with Total and Bioaccessible Concentrations of Cadmium and Lead in Urban Park Soils},
+ journal = {Bulletin of Environmental Contamination and Toxicology},
+ year = {2023},
+ url = {https://pubmed.ncbi.nlm.nih.gov/36907936/}
+}
+
+@article{Nguyen2019,
+ author = {Christine C Nguyen and Cody N Hugie and Molly L Kile and Tala Navab-Daneshmand},
+ title = {Association between heavy metals and antibiotic-resistant human pathogens in environmental reservoirs: A review},
+ journal = {Frontiers of Environmental Science & Engineering},
+ year = {2019},
+ url = {https://doi.org/10.1007/s11783-019-1129-0}
+}
+
@Manual{rmarkdown2021,
title = {rmarkdown: Dynamic Documents for R},
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
@@ -6,6 +78,30 @@ @Manual{rmarkdown2021
url = {https://github.com/rstudio/rmarkdown},
}
+@article{Russell2007,
+ author = {Susan H Russell and Mary P Hancock and James McCullough},
+ title = {Benefits of Undergraduate Research Experiences},
+ journal = {Science},
+ year = {2007},
+ url = {https://doi.org/10.1126/science.1140384}
+}
+
+@article{Sun2021,
+ author = {Fulin Sun and Zhantang Xu and Leilei Fan},
+ title = {Response of heavy metal and antibiotic resistance genes and related microorganisms to different heavy metals in activated sludge},
+ journal = {Journal of Environmental Management},
+ year = {2021},
+ url = {https://doi.org/10.1016/j.jenvman.2021.113754}
+}
+
+@article{Wang2022,
+ author = {Xiaoyu Wang and Gavin F Birch and Enfeng Liu},
+ title = {Traffic emission dominates the spatial variations of metal contamination and ecological-health risks in urban park soil},
+ journal = {Chemosphere},
+ year = {2022},
+ url = {https://pubmed.ncbi.nlm.nih.gov/35240153/}
+}
+
@Book{Xie2018,
title = {R Markdown: The Definitive Guide},
author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
@@ -25,3 +121,11 @@ @Book{Xie2020
note = {ISBN 9780367563837},
url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}
+
+@article{Yan2020,
+ author = {Changchun Yan and Fei Wang and Huanhuan Geng and Haijun Liu and Shengyan Pu and Zhijun Tian and Huilun Chen and Beihai Zhou and Rongfang Yuan and Jun Yao},
+ title = {Integrating high-throughput sequencing and metagenome analysis to reveal the characteristic and resistance mechanism of microbial community in metal contaminated sediments},
+ journal = {Science of the Total Environment},
+ year = {2020},
+ url = {https://doi.org/10.1016/j.scitotenv.2019.136116}
+}
diff --git a/index.Rmd b/index.Rmd
index 0ae4626..4c1b838 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -1,40 +1,46 @@
---
-title: "AnVIL Book Name"
+title: "BioDIGS in the Classroom: Antimicrobial Resistance"
date: "`r format(Sys.time(), '%B %d, %Y')`"
site: bookdown::bookdown_site
documentclass: book
bibliography: book.bib
biblio-style: apalike
link-citations: yes
-description: Description about Course/Book.
-favicon: assets/AnVIL_style/anvil_favicon.ico
+description: "This is a companion training guide for BioDIGS, a GDSCN project."
+favicon: assets/GDSCN_style/gdscn_favicon.ico
---
# About this Book {-}
-This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Learn more about AnVIL by visiting https://anvilproject.org or reading the [article in Cell Genomics](https://www.sciencedirect.com/science/article/pii/S2666979X21001063).
+This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. In this module, students will investigate whether metagenomic samples from the BioDIGS project contain either antimicrobial resistance genes or biosynthesis genes. They will run analyses using ABRicate as implemented on Galaxy. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website [here](https://biodigs.org/) for more information about this collaborative, distributed research project, including how you can get involved!
-## Skills Level {-}
+The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives [here](https://www.gdscn.org/home).
+
+```{r echo=FALSE, fig.alt="BioDIGS logo", out.width='300px', fig.align='center'}
+knitr::include_graphics("https://raw.githubusercontent.com/fhdsl/GDSCN_BioDIGS_Book/main/assets/GDSCN_style/logo_BioDIGS_final.png")
+```
+
+## Skills Level
+
+The activities in this guide are written for undergraduate students and beginning graduate students.
::: {.notice}
_Genetics_
-
+
_Programming skills_
:::
-## AnVIL Collection {-}
+## Platform
-Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/
+The activities in this guide are demonstrated on NHGRI's [AnVIL](https://anvilproject.org/) cloud computing platform. AnVIL is the preferred computing platform for the GDSCN. However, all of these activities can be done using your personal installation of R or using the online [Galaxy](usegalaxy.org) portal.
-# Learning Objectives {-}
+Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/
-
+## Data
-
-
-
+The data generated by the BioDIGS project is available through the [BioDIGS website](biodigs.org), as well as through an [AnVIL workspace](https://anvilproject.org).
-
+Data about the soil itself as well as soil metal content was generated by the [Delaware Soil Testing Program](https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/) at the University of Delaware. Sequences were generated by the [Johns Hopkins University Genetic Resources Core Facility](https://grcf.jhmi.edu/) and by [PacBio](https://www.pacb.com/).
