From 0e9d1ebfe7dcedc81d5e467654a928511b961a60 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 11 Nov 2022 11:00:53 -0500 Subject: [PATCH 01/17] copy over example audience and context --- 01-instructor_guide.Rmd | 144 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 144 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 3e65cee1..97f51043 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -1 +1,145 @@ # (PART\*) Instructor Guide {-} + +## Audience and Context {-} + +From SARS book + +**Audience** + +- Undergraduate biology majors +- Graduate students with less exposure to bioinformatics + +**Prerequisites** + +- Layman understanding of genetics (understanding of DNA, genes, trait inheritance) +- Some previous exposure to the central dogma of molecular biology + +**Class Type** + +- Lab (computer-based) +- Homework for a Lecture + +**Class Size** + +- 1-50 + +**Lesson Duration** + +- 20-30 minute pre-lab lecture +- 3 hour lab for undergraduate students +- 1 hour lab for graduate students +- Additional short lecture modules + +**Assessment Type** + +- Short answer questions at each lab stage + +**Lesson Length** + +- One class period + +----- + +From CourseSource + + From 22255245e15c5eb87c605d2034d7ea6da96077c8 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 14 Nov 2022 13:49:32 -0500 Subject: [PATCH 02/17] add teaching recommendations --- 01-instructor_guide.Rmd | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 97f51043..2b9b21ce 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -1,5 +1,13 @@ # (PART\*) Instructor Guide {-} +## Teaching Recommendations + +This exercise is designed to be used either + +1. As a stand-alone "taste of R", to introduce students to the field of data science, give them an idea of what a data scientist's day-to-day work looks like, and help students see it as something they could do. + +2. As an entry point for a more in-depth course or workshop. In this case we recommend following up on important topics using additional resources (such as [R for Data Science](https://r4ds.had.co.nz/)). The `swirl` lessons are great for letting students work through the basics in a "real" R environment where they get immediate feedback, but they are hard for students to refer back to later. We find `swirl` most useful for giving students a first look at the big ideas, along with practice typing commands into the console. This sets them up well for a more in-depth treatment over the subsequent course/workshop sessions. + ## Audience and Context {-} From SARS book From 65229b0ca40c68189ab1859d5142f33cca823b67 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 14 Nov 2022 19:00:52 -0500 Subject: [PATCH 03/17] fix numbering --- 01-instructor_guide.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 2b9b21ce..4fc1d8e4 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -1,6 +1,6 @@ # (PART\*) Instructor Guide {-} -## Teaching Recommendations +## Teaching Recommendations {-} This exercise is designed to be used either From 21dedd0589796eb6c0ee61bfd4608347d3a6bb17 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 14 Nov 2022 19:12:10 -0500 Subject: [PATCH 04/17] weird rendering of headers --- 01-instructor_guide.Rmd | 8 -------- 1 file changed, 8 deletions(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 4fc1d8e4..97f51043 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -1,13 +1,5 @@ # (PART\*) Instructor Guide {-} -## Teaching Recommendations {-} - -This exercise is designed to be used either - -1. As a stand-alone "taste of R", to introduce students to the field of data science, give them an idea of what a data scientist's day-to-day work looks like, and help students see it as something they could do. - -2. As an entry point for a more in-depth course or workshop. In this case we recommend following up on important topics using additional resources (such as [R for Data Science](https://r4ds.had.co.nz/)). The `swirl` lessons are great for letting students work through the basics in a "real" R environment where they get immediate feedback, but they are hard for students to refer back to later. We find `swirl` most useful for giving students a first look at the big ideas, along with practice typing commands into the console. This sets them up well for a more in-depth treatment over the subsequent course/workshop sessions. - ## Audience and Context {-} From SARS book From a375a1100cde137c22423961d9e905727d43e196 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 15 Nov 2022 13:43:33 -0500 Subject: [PATCH 05/17] trying to fix headings --- index.Rmd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/index.Rmd b/index.Rmd index 18e0691d..36fc6d98 100644 --- a/index.Rmd +++ b/index.Rmd @@ -27,6 +27,8 @@ _Programming skills_ ## Learning Objectives {-} +Does adding text here fix the weird headings? + From 4c44268d106bb876c67014ce690c24fff25d3ef0 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 15 Nov 2022 13:51:07 -0500 Subject: [PATCH 06/17] try deleting the html comments --- index.Rmd | 8 -------- 1 file changed, 8 deletions(-) diff --git a/index.Rmd b/index.Rmd index 36fc6d98..eeb62544 100644 --- a/index.Rmd +++ b/index.Rmd @@ -28,11 +28,3 @@ _Programming skills_ ## Learning Objectives {-} Does adding text here fix the weird headings? - - - - - - - - From ebe9a48d42f5d87d3f0d77464f10f418fccbf88d Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 15 Nov 2022 13:56:40 -0500 Subject: [PATCH 07/17] try adding newline --- index.Rmd | 1 + 1 file changed, 1 insertion(+) diff --git a/index.Rmd b/index.Rmd index eeb62544..a1c7e873 100644 --- a/index.Rmd +++ b/index.Rmd @@ -28,3 +28,4 @@ _Programming skills_ ## Learning Objectives {-} Does adding text here fix the weird headings? + From 8204ac9a3dfd959547608bc92f23099352eb20f0 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 15 Nov 2022 14:03:13 -0500 Subject: [PATCH 08/17] try adding chapter heading --- 01-instructor_guide.Rmd | 2 ++ 1 file changed, 2 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 97f51043..ff4fdcf4 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -1,5 +1,7 @@ # (PART\*) Instructor Guide {-} +# Do I need a chapter heading? + ## Audience and Context {-} From SARS book From 1fad7855e772216702109e9f7a23149410ec319e Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 15 Nov 2022 14:12:30 -0500 Subject: [PATCH 09/17] add teaching recommendations --- 01-instructor_guide.Rmd | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index ff4fdcf4..0729e575 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -1,6 +1,11 @@ # (PART\*) Instructor Guide {-} -# Do I need a chapter heading? +# Teaching Recommendations {-} + +This exercise is designed to be used either + +1. As a stand-alone "taste of R", to introduce students to the field of data science, give them an idea of what a data scientist's day-to-day work looks like, and help students see it as something they could do. +1. As an entry point for a more in-depth course or workshop. In this case we recommend following up on important topics using additional resources (such as [R for Data Science](https://r4ds.had.co.nz/)). The `swirl` lessons are great for letting students work through the basics in a "real" R environment where they get immediate feedback, but they are hard for students to refer back to later. We find `swirl` most useful for giving students a first look at the big ideas, along with practice typing commands into the console. This sets them up well for a more in-depth treatment over the subsequent course/workshop sessions. ## Audience and Context {-} From 7c25710c1ba4b6e74a3eb48de62bc4ca6244459f Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 15 Nov 2022 14:34:46 -0500 Subject: [PATCH 10/17] fix formatting --- 01-instructor_guide.Rmd | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 0729e575..d5a9b9c4 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -1,9 +1,11 @@ # (PART\*) Instructor Guide {-} -# Teaching Recommendations {-} +# Teaching Recommendations This exercise is designed to be used either +
+ 1. As a stand-alone "taste of R", to introduce students to the field of data science, give them an idea of what a data scientist's day-to-day work looks like, and help students see it as something they could do. 1. As an entry point for a more in-depth course or workshop. In this case we recommend following up on important topics using additional resources (such as [R for Data Science](https://r4ds.had.co.nz/)). The `swirl` lessons are great for letting students work through the basics in a "real" R environment where they get immediate feedback, but they are hard for students to refer back to later. We find `swirl` most useful for giving students a first look at the big ideas, along with practice typing commands into the console. This sets them up well for a more in-depth treatment over the subsequent course/workshop sessions. From 4dcc2a06d1733e23d30ca57bcb20dade7cc94d32 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 28 Nov 2022 15:03:50 -0500 Subject: [PATCH 11/17] add computing requirements --- 01-instructor_guide.Rmd | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index d5a9b9c4..0d4a6339 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -152,3 +152,14 @@ o Reveals prior knowledge o Requires student to do the bulk of the work --> + +## Lesson Plan + +## Computing Requirements + +- RStudio +- R packages + - `swirl` + - `dplyr` + +This book provides instructions on how to set these up in the cloud using the [AnVIL platform](https://anvil.terra.bio/), so that your students will not need to install anything. Depending on your needs, you might decide to run this activity on a different cloud provider, such [Posit Cloud](https://posit.cloud/) (formerly RStudio Cloud), or have your students install RStudio themselves. From 4ddf478e4091abbab52b22200fc6c55ae61b30a0 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 2 Dec 2022 13:53:13 -0500 Subject: [PATCH 12/17] move intro paragraphs --- 01-instructor_guide.Rmd | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 0d4a6339..565572cf 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -2,6 +2,10 @@ # Teaching Recommendations +The primary goal of this exercise is to get students comfortable interacting with the R console. Students will complete several `swirl` lessons introducing basic R concepts, and then apply their new skills by conducting a brief exploration of a dataframe. + +The `swirl` lessons touch on several additional R commands and concepts beyond those mentioned in the learning objectives and provide a useful starting point for going deeper if you desire. Additional `swirl` lessons can be found at the [swirl Course Network](http://swirlstats.com/scn/). + This exercise is designed to be used either
From a7cee1d29d3b65a6e709c070eb2f3986c0a77eed Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Fri, 2 Dec 2022 14:12:33 -0500 Subject: [PATCH 13/17] remove linebreak --- 01-instructor_guide.Rmd | 2 -- 1 file changed, 2 deletions(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 565572cf..196baebf 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -8,8 +8,6 @@ The `swirl` lessons touch on several additional R commands and concepts beyond t This exercise is designed to be used either -
- 1. As a stand-alone "taste of R", to introduce students to the field of data science, give them an idea of what a data scientist's day-to-day work looks like, and help students see it as something they could do. 1. As an entry point for a more in-depth course or workshop. In this case we recommend following up on important topics using additional resources (such as [R for Data Science](https://r4ds.had.co.nz/)). The `swirl` lessons are great for letting students work through the basics in a "real" R environment where they get immediate feedback, but they are hard for students to refer back to later. We find `swirl` most useful for giving students a first look at the big ideas, along with practice typing commands into the console. This sets them up well for a more in-depth treatment over the subsequent course/workshop sessions. From 09edc45544bdc1b32e4a6e911c09b87adff86948 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Mon, 5 Dec 2022 13:51:18 -0500 Subject: [PATCH 14/17] reorder teaching recommendations intro --- 01-instructor_guide.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 196baebf..0fed1d9c 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -4,13 +4,13 @@ The primary goal of this exercise is to get students comfortable interacting with the R console. Students will complete several `swirl` lessons introducing basic R concepts, and then apply their new skills by conducting a brief exploration of a dataframe. -The `swirl` lessons touch on several additional R commands and concepts beyond those mentioned in the learning objectives and provide a useful starting point for going deeper if you desire. Additional `swirl` lessons can be found at the [swirl Course Network](http://swirlstats.com/scn/). - This exercise is designed to be used either 1. As a stand-alone "taste of R", to introduce students to the field of data science, give them an idea of what a data scientist's day-to-day work looks like, and help students see it as something they could do. 1. As an entry point for a more in-depth course or workshop. In this case we recommend following up on important topics using additional resources (such as [R for Data Science](https://r4ds.had.co.nz/)). The `swirl` lessons are great for letting students work through the basics in a "real" R environment where they get immediate feedback, but they are hard for students to refer back to later. We find `swirl` most useful for giving students a first look at the big ideas, along with practice typing commands into the console. This sets them up well for a more in-depth treatment over the subsequent course/workshop sessions. +The `swirl` lessons touch on several additional R commands and concepts beyond those mentioned in the learning objectives and provide a useful starting point for going deeper if you desire. Additional `swirl` lessons can be found at the [swirl Course Network](http://swirlstats.com/scn/). + ## Audience and Context {-} From SARS book From 416b86ae6ed8ae7a48b8dd02fac1be68cb0f5221 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 24 Jan 2023 14:46:23 -0500 Subject: [PATCH 15/17] uncomment CourseSource context fields --- 01-instructor_guide.Rmd | 173 ++++++++++++++++++++-------------------- 1 file changed, 85 insertions(+), 88 deletions(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 0fed1d9c..a8347e4c 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -53,107 +53,104 @@ From SARS book From CourseSource - +- [ ] Motivates student to learn material +- [ ] Focuses student on the material to be learned +- [ ] Develops supportive community of learners +- [ ] Leverages differences among learners +- [ ] Reveals prior knowledge +- [ ] Requires student to do the bulk of the work + ## Lesson Plan From a45bcda60c6ebfe84f296f97d11d4c3c49083d40 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 24 Jan 2023 14:54:28 -0500 Subject: [PATCH 16/17] fix bullets --- 01-instructor_guide.Rmd | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index a8347e4c..2c3b467a 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -54,6 +54,7 @@ From SARS book From CourseSource Course Level + - [ ] Introductory - [ ] Upper Level - [ ] Graduate @@ -61,6 +62,7 @@ Course Level - [ ] Other Audience + - [ ] Life Sciences Major - [ ] Physics or Engineering Major - [ ] Non-Life Sciences Major @@ -72,6 +74,7 @@ Audience - [ ] Other Assessment Type + - [ ] Assessment of individual student performance - [ ] Assessment of student groups/teams - [ ] Assignment @@ -111,6 +114,7 @@ Assessment Type - [ ] Other Key Scientific Process Skills + - [ ] Reading research papers - [ ] Reviewing prior research - [ ] Asking a question @@ -124,6 +128,7 @@ Key Scientific Process Skills - [ ] Communicating results Pedagogical Approaches + - [ ] Think-Pair-Share - [ ] Brainstorming - [ ] Case Study @@ -140,10 +145,12 @@ Pedagogical Approaches - [ ] Other Bloom’s Cognitive Level (based on learning objectives & assessments) + - [ ] Foundational: factual knowledge & comprehension - [ ] Application & Analysis Principles of how people learn + - [ ] Motivates student to learn material - [ ] Focuses student on the material to be learned - [ ] Develops supportive community of learners From 27671a067890de3cdad55e3eab22c645f05946c6 Mon Sep 17 00:00:00 2001 From: KatherineCox Date: Tue, 24 Jan 2023 21:40:26 -0500 Subject: [PATCH 17/17] add remaining CourseSource fields --- 01-instructor_guide.Rmd | 46 +++++++++++++++++++++++++++++++++++++---- 1 file changed, 42 insertions(+), 4 deletions(-) diff --git a/01-instructor_guide.Rmd b/01-instructor_guide.Rmd index 2c3b467a..2a0623f7 100644 --- a/01-instructor_guide.Rmd +++ b/01-instructor_guide.Rmd @@ -28,7 +28,6 @@ From SARS book **Class Type** - Lab (computer-based) -- Homework for a Lecture **Class Size** @@ -45,9 +44,6 @@ From SARS book - Short answer questions at each lab stage -**Lesson Length** - -- One class period ----- @@ -73,6 +69,47 @@ Audience - [ ] University - [ ] Other +Class Type + +- [ ] Lecture +- [ ] Lab +- [ ] Seminar +- [ ] Discussion Section +- [ ] On-line +- [ ] Other + +Class Size + +- [ ] 1-50 +- [ ] 51-100 +- [ ] 101+ + +Lesson Length + +- [ ] Portion of one class period +- [ ] One class period +- [ ] Multiple class periods +- [ ] One term (semester or quarter) +- [ ] One year +- [ ] Other + +Vision and Change Core Competencies + +- [ ] Ability to apply the process of science +- [ ] Ability to use quantitative reasoning +- [ ] Ability to use modeling and simulation +- [ ] Ability to tap into the interdisciplinary nature of science +- [ ] Ability to communicate and collaborate with other disciplines +- [ ] Ability to understand the relationship between science and society + +Vision and Change Core Concepts + +- [ ] Evolution +- [ ] Structure and Function +- [ ] Information flow, exchange and storage +- [ ] Pathways and transformations of energy and matter +- [ ] Systems + Assessment Type - [ ] Assessment of individual student performance @@ -148,6 +185,7 @@ Bloom’s Cognitive Level (based on learning objectives & assessments) - [ ] Foundational: factual knowledge & comprehension - [ ] Application & Analysis +- [ ] Synthesis/Evaluation/Creation Principles of how people learn