Merge pull request #11 from jhudsl/learning-objectives

Add learning objectives

index.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "GDSCN: Intro R with swirl "
+title: "Intro R with swirl "
 date: "`r format(Sys.time(), '%B %d, %Y')`"
 site: bookdown::bookdown_site
 documentclass: book
@@ -10,10 +10,13 @@ description: "This book provides a lab exercise that introduces students to the
 favicon: assets/GDSCN_style/gdscn_favicon.ico
 ---
 
-# About this Course {-}
+# About {-}
 
-This book is part of a series of books for the [The Genomic Data Science Community Network (GDSCN)](https://www.gdscn.org/home).  GDSCN is a group of educators gathered with the aim to bring genomic data science education to students at diverse institutions.
+In this exercise, students are introduced to the basics of R using the `swirl` package (https://swirlstats.com), which teaches students R from within the R console.  The primary goal of this exercise is to get students comfortable interacting with the R console.
 
+```{r, echo=FALSE, fig.alt="swirl logo"}
+knitr::include_graphics("assets/swirl_logo.png")
+```
 
 ## Skills Level {-} 
 
@@ -25,12 +28,130 @@ _Programming skills_
 **Novice**: no programming experience needed
 :::
 
+## Format {-}
+
+<!--
+Class Type should be one of the following (from CourseSource):
+- Lecture
+- Lab
+- Seminar
+- Discussion Section
+- On-line
+- Other
+-->
+
+<!--
+Lesson Length should be one of the following (from CourseSource):
+- Portion of one class period
+- One class period
+- Multiple class periods
+- One term (semester or quarter)
+- One year
+- Other
+
+You can then provide addtional details; e.g.
+
+- **Lesson Length:** One class period (2-3 hr lab)
+    - 40 min setup and introduction (for shorter lab periods, these can be done ahead of time)
+    - 2 hr core lab exercises
+    - Optional 20 min "challenge" exercise
+
+-->
+
+- **Class Type:** Lab (computer based)
+- **Lesson Length:** One class period (2-3 hr lab)
+    - 40 min setup and introduction (for shorter lab periods, these can be done ahead of time)
+    - 2 hr core lab exercises
+    - Optional 20 min "challenge" exercise
+
 ## Learning Objectives {-}
 
-<!-- Learning objectives for this activity come from the [Genetics Core Competencies](https://genetics-gsa.org/education/genetics-learning-framework/): -->
+- Open RStudio and locate important panels (R console, Help)
+- Run commands in the R console
+- Explain what vectors and dataframes are in R
+- Use common R commands to work with R objects (e.g. assign, print, subset, math operations)
+- Explore a dataset using base R commands (e.g. `dim`, `summary`, `str`)
+
+## Core Competencies {-}
+
+This activity addresses the following core concepts and competencies:
+
+```{r, echo=FALSE}
+competencies <- tibble::tribble(
+  ~source, ~competencies,
+  
+  "**Vision and Change**",  paste(
+                              #"Concepts\n",
+                              # "- **1**: EVOLUTION: The diversity of life evolved over time by processes of mutation, selection, and genetic change",
+                              # "- **2**: STRUCTURE AND FUNCTION: Basic units of structure define the function of all living things",
+                              # "- **3**: INFORMATION FLOW, EXCHANGE, AND STORAGE: The growth and behavior of organisms are activated through the expression of genetic information in context",
+                              # "- **4**: PATHWAYS AND TRANSFORMATIONS OF ENERGY AND MATTER: Biological systems grow and change by processes based upon chemical transformation pathways and are governed by the laws of thermodynamics",
+                              # "- **5**: SYSTEMS: Living systems are interconnected and interacting.",
+                              
+                              "Competencies\n",
+                              # "- **1**: Ability to apply the process of science",
+                              "- **2**: Ability to use quantitative reasoning",
+                              # "- **3**: Ability to use modeling and simulation",
+                              "- **4**: Ability to tap into the interdisciplinary nature of science",
+                              # "- **5**: Ability to communicate and collaborate with other disciplines",
+                              # "- **6**: Ability to understand the relationship between science and society",
+                            sep="\n"),
+
+
+#   "**Genetics**",         paste(
+                              # "Concepts\n",
+                              # "- How is DNA organized?",
+                              # "- What are the molecular components and mechanisms necessary to preserve and duplicate an organism’s genome?",
+                              # "- What are the mechanisms by which an organism’s genome is passed on to the next generation?",
+                              # "- How can one deduce information about genes, alleles, and gene functions from analysis of genetic crosses and patterns of inheritance?",
+                              # "- How does the phenomenon of linkage affect the assortment of alleles during meiosis?",
+                              # "- How is genetic information expressed so it affects an organism’s structure and function?",
+                              # "- How can gene activity be altered in the absence of DNA changes?",
+                              # "- How do genes and genomes control changes in an organism’s structure and function throughout its life cycle?",
+                              # "- How do different types of mutations affect genes and the corresponding mRNAs and proteins?",
+                              # "- What are the processes that can affect the frequency of genotypes and phenotypes in a population over time?",
+                              # "- How do the results of molecular genetic studies in model organisms help us understand aspects of human genetics and genetic diseases?",
+                              # "- What experimental methods are commonly used to analyze gene structure, gene expression, gene function, and genetic variants?",
+                              
+                              # "Competencies\n",
+                              # "- Locate, read, and comprehend primary literature research papers on genetics topics",
+                              # "- Implement observational strategies to formulate a question",
+                              # "- Generate testable hypotheses",
+                              # "- Design an experiment using appropriate controls and appropriate sample sizes",
+                              # "- Gather and evaluate experimental evidence, including qualitative and quantitative data",
+                              # "- Apply statistical methods when analyzing their data, and use patterns to construct a model",
+                              # "- Generate and interpret graphs displaying experimental results",
+                              # "- Critique large data sets and use bioinformatics to assess genetics data",
+                              # "- Communicate experimental results effectively, including writing research papers and giving presentations",
+                              # "- Effectively explain genetics concepts to different audiences",
+                              # "- Tap into the interdisciplinary nature of science",
+                              # "- Identify and critique scientific issues relating to society or ethics",
+#                           sep="\n"),
+
+
+  "**Bioinformatics**",      paste(
+                               # "- **C1**: Explain the role of computation and data mining in addressing hypothesis-driven and hypothesis-generating questions within the life sciences",
+                               # "- **C2**: Summarize key computational concepts, such as algorithms and relational databases, and their applications in the life sciences",
+                               # "- **C3**: Apply statistical concepts used in bioinformatics",
+                               # "- **C4**: Use bioinformatics tools to examine complex biological problems in evolution, information flow, and other important areas of biology",
+                               # "- **C5**: Find, retrieve, and organize various types of biological data",
+                               # "- **C6**: Explore and/or model biological interactions, networks and data integration using bioinformatics",
+                               "- **C7**: Use command-line bioinformatics tools and write simple computer scripts",
+                               # "- **C8**: Describe and manage biological data types, structure, and reproducibility",
+                               # "- **C9**: Interpret the ethical, legal, medical, and social implications of biological data",
+                             sep="\n")
+)
+
+knitr::kable(competencies, col.names = NULL, format = "html")
+```
+
+Core concepts and competencies are taken from the following sources:
+
+  - [Vision and Change in Undergraduate Biology Education](https://visionandchange.org/) AAAS report
+  - [Genetics Core Competencies](https://genetics-gsa.org/education/genetics-learning-framework/) by [GSA](https://genetics-gsa.org/)
+  - [Bioinformatics core competencies for undergraduate life sciences education](https://doi.org/10.1371/journal.pone.0196878) by [NIBLSE](https://qubeshub.org/community/groups/niblse)
+
+## GDSCN Collection {-}
 
-<!-- - Objective 1 -->
-<!-- - Objective 2 -->
-<!-- - Objective 3 -->
+This exercise is part of a collection of teaching resources developed through the *Genomic Data Science Community Network* (GDSCN). GDSCN works towards a vision where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research.  Learn more about GDSCN by visiting https://www.gdscn.org/home or reading the [article in Genome Research](https://doi.org/10.1101/gr.276496.121).
 
-<!-- Please also see the Bioinformatics core competencies for undergraduate life sciences education from NIBLSE: https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0196878.t002 -->

resources/dictionary.txt

@@ -1,5 +1,7 @@
+AAAS
 AnVIL
 autocomplete
+Bioinformatics
 BIPOC
 Bloomberg
 callout
@@ -13,6 +15,7 @@ Irizarry
 mentorship
 NCI
 NHGRI
+NIBLSE
 Onboarding
 OTTR
 ottrpal