creating-project-overview-chapter

01-intro.Rmd

@@ -11,11 +11,6 @@ This is a companion training guide for BioDIGS, a GDSCN project that brings a re
 
 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).
 
-## Motivation
-
-One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers ^1. It can also lead to improved scientific reasoning and increased academic performance overall ^2. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science ^3 ^4.
-
-The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education.
 
 ## Target Audience
 
@@ -28,20 +23,3 @@ The activities in this guide are demonstrated on NHGRI's [AnVIL](https://anvilpr
 ## 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). 
-## Who did the soil sampling?
-
-Soil sampling for this project was done by both faculty and student volunteers from schools that aren't traditional R1 research institutions. 
-
-## Where is the funding from? 
-
-Funding for this project is through Contract # 75N92022P00232 from the National Human Genome Research Institute awarded to Johns Hopkins University.
-
-## References
-
-1: Russell et al. 2007: https://doi.org/10.1126/science.1140384
-
-2: Buffalari et al. 2020: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040836/
-
-3: Canner et al. 2017: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398168/
-
-4: GDSCN 2022: https://doi.org/10.1101/gr.276496.121

02-instructor_guide.Rmd

@@ -1,9 +1,7 @@
 
 # A new chapter
 
-*If you haven't yet read the getting started Wiki pages; [start there](https://github.com/jhudsl/OTTR_Template/wiki/Getting-started)
 
-Every chapter needs to start out with this chunk of code:
 
 ```{r, include = FALSE}
 ottrpal::set_knitr_image_path()
@@ -96,9 +94,6 @@ This works:
 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://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf).
 
 Or this:
 

03-BioDIGS_project_overview.Rmd

@@ -1,52 +1,23 @@
-# AnVIL Module Library
+## Motivation
 
-There are several pieces of content that are useful across multiple books, such as "How to Create a Workspace".  To reduce maintenance burden, the `AnVIL_Template` repository has a collection of `_child` R Markdown documents that can be included in your books.
+One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student's interest in pursuing STEM careers ^1. It can also lead to improved scientific reasoning and increased academic performance overall ^2. However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science ^3 ^4.
 
-You can see all the available AnVIL modules in the [AnVIL_Template book](https://jhudatascience.org/AnVIL_Template/)
+The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education.
 
-## Include using `cow::borrow_chapter()`
+## Who did the soil sampling?
 
-To add a module to your book, include a code chunk with the `cow::borrow_chapter()` function, specifying the file for the module you want to borrow and the repository you want to borrow it from (the `AnVIL_Template` repository).
+Soil sampling for this project was done by both faculty and student volunteers from schools that aren't traditional R1 research institutions. 
 
-See the OTTR_Template [wiki page](https://github.com/jhudsl/OTTR_Template/wiki/Borrowing-chapters-between-courses) for the most recent instructions and additional details.
+## Where is the funding from? 
 
-Here is an example of including the `_child_workspace_create.Rmd` with `cow::borrow_chapter()`
+Funding for this project is through Contract # 75N92022P00232 from the National Human Genome Research Institute awarded to Johns Hopkins University.
 
-```{r, echo = FALSE, results='asis'}
-cow::borrow_chapter(
-  doc_path = "child/_child_workspace_create.Rmd",
-  repo_name = "jhudsl/AnVIL_Template"
-)
-```
+## References
 
-## Background Highlighting for Borrowed Chapters
+1: Russell et al. 2007: https://doi.org/10.1126/science.1140384
 
-You can use the `borrowed_chunk` [custom div block](https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html) to highlight borrowed content or any other content you choose.
+2: Buffalari et al. 2020: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040836/
 
-**Basic format:**
+3: Canner et al. 2017: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398168/
 
-```
-:::: {.borrowed_chunk}
-Code/Content here
-::::
-```
-
-**Rendered with highlighting:**
-
-:::: {.borrowed_chunk}
-```{r, echo = FALSE, results='asis'}
-cow::borrow_chapter(
-  doc_path = "child/_child_google_create_account.Rmd",
-  repo_name = "jhudsl/AnVIL_Template"
-)
-```
-::::
-
-**Rendered without highlighting:**
-
-```{r, echo = FALSE, results='asis'}
-cow::borrow_chapter(
-  doc_path = "child/_child_google_create_account.Rmd",
-  repo_name = "jhudsl/AnVIL_Template"
-)
-```
+4: GDSCN 2022: https://doi.org/10.1101/gr.276496.121