From 40a4333f2c751468b3d85c8193ec87d24509f747 Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 14 Jun 2024 17:30:31 -0400 Subject: [PATCH 1/6] start filling out a little --- 01-intro.Rmd | 3 ++- 01b-overview.Rmd | 28 ++++++++++++++++++++++++++++ _bookdown.yml | 3 ++- 3 files changed, 32 insertions(+), 2 deletions(-) create mode 100644 01b-overview.Rmd diff --git a/01-intro.Rmd b/01-intro.Rmd index 886eb52..7f3cbf2 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -8,10 +8,11 @@ ottrpal::set_knitr_image_path() ## Motivation +This course aims to provide motivations for learning computational skills and discuss specific examples or ways computational skills could benefit or supplement wet lab work. ## Target Audience -The course is intended for ... +The course is intended for wet lab researchers who have very little to no computational experience (for example: users of Excel or GraphPad Prism, but non-"coders") ## Curriculum diff --git a/01b-overview.Rmd b/01b-overview.Rmd new file mode 100644 index 0000000..0f02816 --- /dev/null +++ b/01b-overview.Rmd @@ -0,0 +1,28 @@ + +```{r, include = FALSE} +ottrpal::set_knitr_image_path() +``` + +# What are computational biology and data science? + +# Motivations for computational work + +# How does a researcher approach computional work? + +# Examples of the application of computational work to wet lab research + +# Rigor and ethics in computional work + +# Why learn computational skills yourself + +# Which computational skills are the most important to prioritize learning as a wet lab scientist + +## Data Wrangling + +## Data Visualization + +## Reproducibility and Transparency + +## Sharing and reusing public data, code, or tools + +In conclusion, the benefits of knowing computational skills as a wet lab scientist ... \ No newline at end of file diff --git a/_bookdown.yml b/_bookdown.yml index be44855..dfe068a 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -1,8 +1,9 @@ book_filename: "Bench to Bytes" chapter_name: "Chapter " -repo: https://github.com/jhudsl/OTTR_Template/ +repo: https://github.com/jhudsl/bench_to_bytes/ rmd_files: ["index.Rmd", "01-intro.Rmd", + "01b-overview.Rmd" "02-DataCleaning.Rmd", "03-DataViz.Rmd", "04-Reproducibility.Rmd", From f733c05968d49b4826330bcf3813a69dfcb045c8 Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 14 Jun 2024 17:40:02 -0400 Subject: [PATCH 2/6] missing comma --- _bookdown.yml | 4 ++-- index.Rmd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/_bookdown.yml b/_bookdown.yml index dfe068a..a656cc4 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -1,9 +1,9 @@ book_filename: "Bench to Bytes" chapter_name: "Chapter " -repo: https://github.com/jhudsl/bench_to_bytes/ +repo: https://github.com/fhdsl/bench_to_bytes/ rmd_files: ["index.Rmd", "01-intro.Rmd", - "01b-overview.Rmd" + "01b-overview.Rmd", "02-DataCleaning.Rmd", "03-DataViz.Rmd", "04-Reproducibility.Rmd", diff --git a/index.Rmd b/index.Rmd index d23fbb2..5d3c6b7 100644 --- a/index.Rmd +++ b/index.Rmd @@ -28,7 +28,7 @@ This course is part of a series of courses for the [Informatics Technology for C This course is available in multiple formats which allows you to take it in the way that best suites your needs. You can take it for certificate which can be for free or fee. -- The material for this course can be viewed without login requirement on this [Bookdown website](LINK HERE). This format might be most appropriate for you if you rely on screen-reader technology. +- The material for this course can be viewed without login requirement on this [course website](https://hutchdatascience.org/bench_to_bytes/). This format might be most appropriate for you if you rely on screen-reader technology. - This course can be taken for [free certification through Leanpub](LINK HERE). - This course can be taken on [Coursera for certification here](LINK HERE) (but it is not available for free on Coursera). -- Our courses are open source, you can find the [source material for this course on GitHub](LINK HERE). +- Our courses are open source, you can find the [source material for this course on GitHub](https://github.com/fhdsl/bench_to_bytes). From 38454aa4cf71f2914649159c7fff8445dedcd894 Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 21 Jun 2024 16:02:05 -0500 Subject: [PATCH 3/6] add edits based off of meeting notes --- 01-intro.Rmd | 15 ++++++++++++++- 01b-overview.Rmd | 36 +++++++++++++++++++++++------------- 2 files changed, 37 insertions(+), 14 deletions(-) diff --git a/01-intro.Rmd b/01-intro.Rmd index 7f3cbf2..b75964a 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -12,12 +12,25 @@ This course aims to provide motivations for learning computational skills and di ## Target Audience -The course is intended for wet lab researchers who have very little to no computational experience (for example: users of Excel or GraphPad Prism, but non-"coders") +The course is intended for wet lab researchers who have very little to no computational research experience (for example: users of Excel or GraphPad Prism, but non-"coders") + +```{r, include=FALSE} +ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0eecfd5_5_25") +``` ## Curriculum The course covers... +```{r, include=FALSE} +ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0eecfd5_5_0") +``` + +## Objectives + +```{r} +ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f3ba2b3c_1_292") +``` ```{r} devtools::session_info() diff --git a/01b-overview.Rmd b/01b-overview.Rmd index 0f02816..878881c 100644 --- a/01b-overview.Rmd +++ b/01b-overview.Rmd @@ -1,28 +1,38 @@ - ```{r, include = FALSE} ottrpal::set_knitr_image_path() ``` +# The who, what, when, where, and why of Computational Biology + +## Learning Objectives + +```{r} +ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g27401a19bd8_1_0") +``` + +## What are computational biology and data science? -# What are computational biology and data science? +## Motivations for computational work in general and to learn computational skills yourself -# Motivations for computational work +## Examples of the application of computational work to wet lab research -# How does a researcher approach computional work? +## The philosophies and best practices of computational work -# Examples of the application of computational work to wet lab research +### Rigor and ethics in computational work -# Rigor and ethics in computional work +## Which computational skills are the most important to prioritize learning as a wet lab scientist -# Why learn computational skills yourself +### Data Wrangling -# Which computational skills are the most important to prioritize learning as a wet lab scientist +### Data Visualization -## Data Wrangling +### Reproducibility and Transparency -## Data Visualization +### Sharing and reusing public data, code, or tools -## Reproducibility and Transparency +In conclusion, the benefits of knowing computational skills as a wet lab scientist ... -## Sharing and reusing public data, code, or tools +```{r} +ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0ffd840_0_3") +``` -In conclusion, the benefits of knowing computational skills as a wet lab scientist ... \ No newline at end of file +Rather than a scientist being a wet-lab researcher or a dry-lab researcher, in the future we hope scientists have and utilize lab and computational skills for their research. From 019ab3b79fc5705cb7e78bbe614d6caae3dbd08a Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 21 Jun 2024 16:11:07 -0500 Subject: [PATCH 4/6] include false --- 01-intro.Rmd | 2 +- 01b-overview.Rmd | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/01-intro.Rmd b/01-intro.Rmd index b75964a..204871e 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -28,7 +28,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgt ## Objectives -```{r} +```{r, include=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f3ba2b3c_1_292") ``` diff --git a/01b-overview.Rmd b/01b-overview.Rmd index 878881c..3d9ef35 100644 --- a/01b-overview.Rmd +++ b/01b-overview.Rmd @@ -5,7 +5,7 @@ ottrpal::set_knitr_image_path() ## Learning Objectives -```{r} +```{r, include=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g27401a19bd8_1_0") ``` @@ -29,9 +29,11 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgt ### Sharing and reusing public data, code, or tools +## Conclusion + In conclusion, the benefits of knowing computational skills as a wet lab scientist ... -```{r} +```{r, include=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0ffd840_0_3") ``` From 08da86823bdda2dfe92f3b60578946b55166f77e Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 21 Jun 2024 16:15:26 -0500 Subject: [PATCH 5/6] echo not include --- 01-intro.Rmd | 6 +++--- 01b-overview.Rmd | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/01-intro.Rmd b/01-intro.Rmd index 204871e..0ff6bb2 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -14,7 +14,7 @@ This course aims to provide motivations for learning computational skills and di The course is intended for wet lab researchers who have very little to no computational research experience (for example: users of Excel or GraphPad Prism, but non-"coders") -```{r, include=FALSE} +```{r, echo=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0eecfd5_5_25") ``` @@ -22,13 +22,13 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgt The course covers... -```{r, include=FALSE} +```{r, echo=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0eecfd5_5_0") ``` ## Objectives -```{r, include=FALSE} +```{r, echo=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f3ba2b3c_1_292") ``` diff --git a/01b-overview.Rmd b/01b-overview.Rmd index 3d9ef35..0d6ee09 100644 --- a/01b-overview.Rmd +++ b/01b-overview.Rmd @@ -5,7 +5,7 @@ ottrpal::set_knitr_image_path() ## Learning Objectives -```{r, include=FALSE} +```{r, echo=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g27401a19bd8_1_0") ``` @@ -33,7 +33,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgt In conclusion, the benefits of knowing computational skills as a wet lab scientist ... -```{r, include=FALSE} +```{r, echo=FALSE} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0ffd840_0_3") ``` From b3ea03b7fcb2c88bece16c7b58b00ab7c7c4616d Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 21 Jun 2024 17:50:22 -0500 Subject: [PATCH 6/6] add some otterpal slide chunk stuff --- 01-intro.Rmd | 6 +++--- 01b-overview.Rmd | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/01-intro.Rmd b/01-intro.Rmd index 0ff6bb2..10fc69a 100644 --- a/01-intro.Rmd +++ b/01-intro.Rmd @@ -14,7 +14,7 @@ This course aims to provide motivations for learning computational skills and di The course is intended for wet lab researchers who have very little to no computational research experience (for example: users of Excel or GraphPad Prism, but non-"coders") -```{r, echo=FALSE} +```{r, echo=FALSE, fig.align='center', out.width="100%", fig.alt="FILL IN TARGET AUDIENCE"} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0eecfd5_5_25") ``` @@ -22,13 +22,13 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgt The course covers... -```{r, echo=FALSE} +```{r, echo=FALSE, fig.align='center', out.width="100%", fig.alt="FILL IN CONCEPTS DISCUSSED"} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0eecfd5_5_0") ``` ## Objectives -```{r, echo=FALSE} +```{r, echo=FALSE, fig.align='center', out.width="100%", fig.alt="FILL IN OBJECTIVES"} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f3ba2b3c_1_292") ``` diff --git a/01b-overview.Rmd b/01b-overview.Rmd index 0d6ee09..d7b8fbe 100644 --- a/01b-overview.Rmd +++ b/01b-overview.Rmd @@ -5,7 +5,7 @@ ottrpal::set_knitr_image_path() ## Learning Objectives -```{r, echo=FALSE} +```{r, echo=FALSE, fig.align='center', out.width="100%", fig.alt="FILL IN LOs"} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g27401a19bd8_1_0") ``` @@ -29,11 +29,11 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgt ### Sharing and reusing public data, code, or tools -## Conclusion +## Summary In conclusion, the benefits of knowing computational skills as a wet lab scientist ... -```{r, echo=FALSE} +```{r, echo=FALSE, fig.align='center', out.width="100%", fig.alt="There are benefits to learning computational skills as a wet lab scientist!"} ottrpal::include_slide("https://docs.google.com/presentation/d/137sOakbsXwN3ovgtlAzZMbQ5a_6ZIg-weTYeQ_Z7DqU/edit#slide=id.g273f0ffd840_0_3") ```