fhdsl · avahoffman · Dec 3, 2025 · Dec 3, 2025 · Dec 3, 2025 · Dec 3, 2025
diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,5 @@
 .Ruserdata
 .DS_Store
 /.quarto/
+
+**/*.quarto_ipynb
diff --git a/module/AOU_ethics.qmd b/module/AOU_ethics.qmd
@@ -6,35 +6,55 @@ output:
 
 ## Overview
 
-These ethics-related questions can be added on to any activity that leverages the [All of Us Data Browser](https://databrowser.researchallofus.org/).
+This module uses the [All of Us Data Browser](https://databrowser.researchallofus.org/) to encourage critical thinking on ethical concepts in human genomics. 
 
-**Duration:** Approximately 1 hour.
+**Duration:** 30 minutes - 1 hour.
 
 ## Learning Objectives
 
 1.  Identify and critique scientific issues relating to society or ethics (see [GSA](https://genetics-gsa.org/education/genetics-learning-framework/) core competencies).
 
-2. Interpret the ethical, legal, medical, and social implications of biological data (see [NIBLSE](https://qubeshub.org/community/groups/niblse/core_competencies) core competencies).
+2.  Interpret the ethical, legal, medical, and social implications of biological data (see [NIBLSE](https://qubeshub.org/community/groups/niblse/core_competencies) core competencies).
 
-## Materials and Setup
+## Prerequisites
 
--   Download the student activity as:
+Students will benefit from some awareness of genetically-based medical conditions and ethics in genomics. We suggest this activity could accompany lectures that discuss these topics. These ethics-related questions can also be added on to any activity that leverages the [All of Us Data Browser](https://databrowser.researchallofus.org/).
 
-    -   [Web page](https://genomicseducation.org/module/AOU_ethics_student_guide.html)
-    -   [Quarto (qmd)](https://github.com/fhdsl/GEMs/blob/main/module/AOU_ethics_student_guide.qmd)
-    -   [Word (docx)](https://github.com/fhdsl/GEMs/raw/main/docs/docx/module/AOU_ethics_student_guide.docx)
-    -   [Google Doc](https://docs.google.com/document/d/1Xi1M9icJUJ2pfxp5pOV4yzQUHfQCM8zo/edit?usp=sharing&ouid=116032995747974603894&rtpof=true&sd=true)
+## Evaluation
 
--   Answer key available [here](https://docs.google.com/document/d/16GiVCWKhVxkKzOUr6XlQ_vdj-tyxBYlIa3lmstzf38Y/edit?usp=sharing). Please message Ava Hoffman (ahoffma2 at fredhutch dot org) to get access.
+GEMs is an NIH-funded program. Part of our mission is understanding the impact of our materials. Please take the time to review our program as an instructor after this activity. We also appreciate you distributing our survey to students before and after they participate in GEMs content.
 
-## Evaluation
+::: callout-tip
+## Help Us Improve!
+
+[Instructor experience survey](https://forms.gle/QExaV8pQ9tWpaiED9)
+
+[Student pre-activity survey](https://genomicseducation.shinyapps.io/student_pre_survey/)
+
+[Student post-activity survey](https://genomicseducation.shinyapps.io/student_post_survey/)
+:::
 
-::: {.callout-tip}
-## Help us improve!
+You can view our IRB approval [here](https://drive.google.com/file/d/16Wx2CxDsmojfWacb2S1SHbYdI3kqBzFX/view?usp=sharing). Feel free to contact the GEMs team with any questions (gems **at** fredhutch **dot** org).
 
-GEMs is an NIH-funded program. Part of our mission is understanding the impact of our materials. Please take the time to review our program as an instructor. We also appreciate you distributing our survey to students after they participate in GEMs content.
+## Materials
 
-[Instructor survey](https://forms.gle/QExaV8pQ9tWpaiED9)
+### Student Activity
 
-Student survey
+You can use this module in several formats. Feel free to adapt to your needs!
+
+-   [Web page](https://genomicseducation.org/module/AOU_ethics_student_guide.html)
+-   [Quarto (qmd)](https://github.com/fhdsl/GEMs/blob/main/module/AOU_ethics_student_guide.qmd)
+-   [Word (docx)](https://github.com/fhdsl/GEMs/raw/main/docs/docx/module/AOU_ethics_student_guide.docx)
+-   [Google Doc](https://docs.google.com/document/d/1Xi1M9icJUJ2pfxp5pOV4yzQUHfQCM8zo/edit?usp=sharing&ouid=116032995747974603894&rtpof=true&sd=true)
+
+Students will need a device that accesses the internet.
+
+::: callout-warning
+## This content contains URLs
+
+We suggest confirming links are still active prior to running this activity.
 :::
+
+### Instructor Materials
+
+An answer key is available [here](https://docs.google.com/document/d/16GiVCWKhVxkKzOUr6XlQ_vdj-tyxBYlIa3lmstzf38Y/edit?usp=sharing). Please message Ava Hoffman (ahoffma2 at fredhutch dot org) to get access.
diff --git a/module/database_detectives.qmd b/module/database_detectives.qmd
@@ -10,7 +10,7 @@ This activity guides students through using publicly-available genomics database
 
 This activity is loosely based on the game Clue. Students need to match four _Drosophila_ genes to the correct experimental data and background research.
 
-**Duration:** 1-3 hours
+**Duration:** 1-3 hours ([help us improve this estimate!](https://forms.gle/jPppG3dSnEQneDEZA))
 
 ## Learning Objectives
 
@@ -22,21 +22,52 @@ This activity is loosely based on the game Clue. Students need to match four _Dr
 
 4. Determine the associations between _Drosophila_ gene homologs and human diseases. 
 
+## Prerequisites
+
+<!-- Example from AOU: -->
+<!-- Students will benefit from some awareness of genetically-based medical conditions and ethics in genomics. We suggest this activity could accompany lectures that discuss these topics. These ethics-related questions can also be added on to any activity that leverages the [All of Us Data Browser](https://databrowser.researchallofus.org/). -->
+
+## Evaluation
+
+GEMs is an NIH-funded program. Part of our mission is understanding the impact of our materials. Please take the time to review our program as an instructor after this activity. We also appreciate you distributing our survey to students before and after they participate in GEMs content.
+
+::: {.callout-tip}
+## Help us improve!
+
+[Instructor survey](https://forms.gle/jPppG3dSnEQneDEZA)
+
+[Student pre-activity survey](https://genomicseducation.shinyapps.io/student_pre_survey/)
+
+[Student post-activity survey](https://genomicseducation.shinyapps.io/student_post_survey/)
+:::
+
+You can view our IRB approval [here](https://drive.google.com/file/d/16Wx2CxDsmojfWacb2S1SHbYdI3kqBzFX/view?usp=sharing). Feel free to contact the GEMs team with any questions (gems **at** fredhutch **dot** org).
+
 ## Materials
 
--   Students will need:
+### Student Activity
+
+You can use this module in several formats. Feel free to adapt to your needs!
 
-    -   An internet connection for this activity. Students will use these websites: [_FlyBase_](https://flybase.org/), [_Mouse Genome Informatics_](https://informatics.jax.org/), [_ZFIN (Zebrafish Information Network _](https://zfin.org/), [_GeneCards_](https://www.genecards.org/), [_OMIM_](https://omim.org/), and [_MalaCards_](https://www.malacards.org/)
+-   [Web page](https://genomicseducation.org/module/database_detectives_student_guide.html)
+-   [Word (docx)](https://github.com/fhdsl/GEMs/raw/main/docs/docx/module/database_detectives_student_guide.docx)
+-   [Google Doc](https://docs.google.com/document/d/1mlyqdhbFCfYPEdiFKX9KH2FCy34EL8Eg/edit?usp=sharing&ouid=101727846555185296348&rtpof=true&sd=true) 
 
--   Download the student activity as:
+Students will need a device that accesses the internet.
 
-    -   [Web page](https://genomicseducation.org/module/database_detectives_student_guide.html)
-    -   [Word (docx)](https://github.com/fhdsl/GEMs/raw/main/docs/docx/module/database_detectives_student_guide.docx)
-    -   [Google Doc](https://docs.google.com/document/d/1mlyqdhbFCfYPEdiFKX9KH2FCy34EL8Eg/edit?usp=sharing&ouid=101727846555185296348&rtpof=true&sd=true) 
+::: callout-warning
+## This content contains URLs
 
--   Google Slides presentation available for borrowing images [here](https://docs.google.com/presentation/d/1fy3FwkSLETnRUdf8huddq2n4qcb6eOyzwVg05dbudII/edit?slide=id.g2c8182c8825_0_50#slide=id.g2c8182c8825_0_50).
+We suggest confirming links are still active prior to running this activity.
 
--   Answer key available [here](https://docs.google.com/document/d/1QLoxy045YQydpZxQfaDCVLSRSi4fU00ceLBDNblAdsA/edit?tab=t.0). Please message Ava Hoffman (ahoffma2 at fredhutch dot org) to get access.
+Students will use these websites: [_FlyBase_](https://flybase.org/), [_Mouse Genome Informatics_](https://informatics.jax.org/), [_ZFIN (Zebrafish Information Network)_](https://zfin.org/), [_GeneCards_](https://www.genecards.org/), [_OMIM_](https://omim.org/), and [_MalaCards_](https://www.malacards.org/)
+:::
+
+### Instructor Materials
+
+A Google Slides presentation is available for borrowing images [here](https://docs.google.com/presentation/d/1fy3FwkSLETnRUdf8huddq2n4qcb6eOyzwVg05dbudII/edit?slide=id.g2c8182c8825_0_50#slide=id.g2c8182c8825_0_50).
+
+An answer key is available [here](https://docs.google.com/document/d/1QLoxy045YQydpZxQfaDCVLSRSi4fU00ceLBDNblAdsA/edit?tab=t.0). Please message Ava Hoffman (ahoffma2 at fredhutch dot org) to get access.
 
 ## Scientific Topics
 
@@ -61,16 +92,3 @@ In addition to working with public genomic databases, students are exposed to th
 - Part 3: Using OMIM and MalaCards
 
 - Part 4: Solving the Data Mystery
-
-## Evaluation
-
-::: {.callout-tip}
-## Help us improve!
-
-GEMs is an NIH-funded program. Part of our mission is understanding the impact of our materials. Please take the time to review our program as an instructor. We also appreciate you distributing our survey to students after they participate in GEMs content.
-
-[Instructor survey](https://forms.gle/jPppG3dSnEQneDEZA)
-
-Student survey
-:::
-
diff --git a/module/family_markers.qmd b/module/family_markers.qmd
@@ -12,35 +12,56 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1dhP4CeUIJAqy3z7m
 
 This activity teaches students to interpret pedigree information and use bioinformatics tools (R) to build pedigrees for tracking disease traits in families. Students will work with real data from a bipolar disorder genetics study to understand how researchers understand risk genes using pedigrees.
 
-**Duration:** Approximately 2-3 hours (depending on student familiarity with R)
+**Duration:** Approximately 2-3 hours (depending on student familiarity with R) ([help us improve this estimate!](https://forms.gle/pgvLDMChG19pGjCq7))
 
 ## Learning Objectives
 
 1.  Interpret pedigree information to determine the suitability of a DNA marker for tracking a disease trait in a family (see [GSA](https://genetics-gsa.org/education/genetics-learning-framework/) learning objectives).
 
 2.  Build a pedigree using bioinformatics tools (R).
 
-## Materials and Setup
+## Prerequisites
 
--   Students will need either:
+<!-- Example from AOU: -->
+<!-- Students will benefit from some awareness of genetically-based medical conditions and ethics in genomics. We suggest this activity could accompany lectures that discuss these topics. These ethics-related questions can also be added on to any activity that leverages the [All of Us Data Browser](https://databrowser.researchallofus.org/). -->
 
-    -   An internet connection for this activity as written (using Posit Cloud)
-    -   A local installation of R or RStudio (with data downloaded and `kinship2` package installed ahead of time)
+## Evaluation
+
+GEMs is an NIH-funded program. Part of our mission is understanding the impact of our materials. Please take the time to review our program as an instructor after this activity. We also appreciate you distributing our survey to students before and after they participate in GEMs content.
+
+::: {.callout-tip}
+## Help us improve!
+
+[Instructor survey](https://forms.gle/pgvLDMChG19pGjCq7)
+
+[Student pre-activity survey](https://genomicseducation.shinyapps.io/student_pre_survey/)
+
+[Student post-activity survey](https://genomicseducation.shinyapps.io/student_post_survey/)
+:::
+
+You can view our IRB approval [here](https://drive.google.com/file/d/16Wx2CxDsmojfWacb2S1SHbYdI3kqBzFX/view?usp=sharing). Feel free to contact the GEMs team with any questions (gems **at** fredhutch **dot** org).
+
+## Materials
 
--   Required R package: `kinship2`
+### Student Activity
 
--   Data hosting: https://genomicseducation.org/data/pedigree_data.csv
+You can use this module in several formats. Feel free to adapt to your needs!
 
--   Download the R student activity as:
+-   [Web page](https://genomicseducation.org/module/family_markers_student_guide.html)
+-   [Quarto (qmd)](https://github.com/fhdsl/GEMs/blob/main/module/family_markers_student_guide.qmd)
+-   [Word (docx)](https://github.com/fhdsl/GEMs/raw/main/docs/docx/module/family_markers_student_guide.docx)
+-   [Google Doc](https://docs.google.com/document/d/1PBGugINV2mOrq-knq5MXPOC-WcQSxnMA/edit?usp=sharing&ouid=116032995747974603894&rtpof=true&sd=true)
 
-    -   [Web page](https://genomicseducation.org/module/family_markers_student_guide.html)
-    -   [Quarto (qmd)](https://github.com/fhdsl/GEMs/blob/main/module/family_markers_student_guide.qmd)
-    -   [Word (docx)](https://github.com/fhdsl/GEMs/raw/main/docs/docx/module/family_markers_student_guide.docx)
-    -   [Google Doc](https://docs.google.com/document/d/1PBGugINV2mOrq-knq5MXPOC-WcQSxnMA/edit?usp=sharing&ouid=116032995747974603894&rtpof=true&sd=true)
+Students will need RStudio, data, and the R package: `kinship2`. This means either:
 
--   Google Slides presentation available for borrowing images [here](https://docs.google.com/presentation/d/1dhP4CeUIJAqy3z7mKxuFzk8b8LhLrPBPHb1bpYpbk3c/edit?usp=sharing).
+-   A device with an internet connection for this activity as written (using Posit Cloud), access to the data hosted at https://genomicseducation.org/data/pedigree_data.csv.
+-   A local installation of R or RStudio, the ability to install the `kinship2` package, and downloaded data from https://genomicseducation.org/data/pedigree_data.csv. Instructors are welcome to download the data and provide it via email or an LMS system if desired.
 
--   Answer key available [here](https://docs.google.com/document/d/1KcX30s2fYzFw16boGVO4MlhSAA2Pr3OzqwmndeO043U/edit?usp=sharing). Please message Ava Hoffman (ahoffma2 at fredhutch dot org) to get access.
+### Instructor Materials
+
+A Google Slides presentation is available for borrowing images [here](https://docs.google.com/presentation/d/1dhP4CeUIJAqy3z7mKxuFzk8b8LhLrPBPHb1bpYpbk3c/edit?usp=sharing).
+
+An answer key is available [here](https://docs.google.com/document/d/1KcX30s2fYzFw16boGVO4MlhSAA2Pr3OzqwmndeO043U/edit?usp=sharing). Please message Ava Hoffman (ahoffma2 at fredhutch dot org) to get access.
 
 ## Scientific Topics
 
@@ -63,15 +84,3 @@ The activity is based a [published research study](https://www.nature.com/articl
 -   Part 3: Adding Diagnostic Information (15-20 minutes)
 
 -   Part 4: Genotype Mapping and Analysis (30-40 minutes)
-
-## Evaluation
-
-::: {.callout-tip}
-## Help us improve!
-
-GEMs is an NIH-funded program. Part of our mission is understanding the impact of our materials. Please take the time to review our program as an instructor. We also appreciate you distributing our survey to students after they participate in GEMs content.
-
-[Instructor survey](https://forms.gle/pgvLDMChG19pGjCq7)
-
-Student survey
-:::