Merge pull request #5 from fhdsl/startShell

work on shell

02-DataCleaning.Rmd

@@ -0,0 +1,15 @@
+# Data cleaning
+
+The first "why computational skill are useful" theme that we'll explore is data cleaning.
+
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}

03-DataViz.Rmd

@@ -0,0 +1,15 @@
+# Data visualization
+
+The second "why computational skill are useful" theme that we'll explore is data visualization
+
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}

04-Reproducibility.Rmd

@@ -0,0 +1,15 @@
+# Reproducibility
+
+The third "why computational skill are useful" theme that we'll explore is reproducibility.
+
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}

05-Sharing.Rmd

@@ -0,0 +1,15 @@
+# Public Data and Code Sharing and Reuse
+
+The final "why computational skill are useful" theme that we'll explore is public data and code sharing and reuse
+
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+## Learning Objectives
+
+This chapter will cover:
+
+- {LO1}
+- {LO2}

README.md

@@ -1,4 +1,4 @@
-# {Course Name}
+# Bench to Bytes
 
 This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).
 
@@ -8,7 +8,7 @@ If you would like to contribute to this course material, take a look at the [OTT
 
 ## About this course
 
-This course introduces {info on what this course introduces}
+This course introduces motivations for learning computational and data science skills that can be beneficial for both wet and dry lab researchers across all scientific fields.
 
 ## Learning Objectives
 

_bookdown.yml

@@ -1,9 +1,12 @@
-book_filename: "Course_Name"
+book_filename: "Bench to Bytes"
 chapter_name: "Chapter "
 repo: https://github.com/jhudsl/OTTR_Template/
 rmd_files: ["index.Rmd",
             "01-intro.Rmd",
-            "02-chapter_of_course.Rmd",
+            "02-DataCleaning.Rmd",
+            "03-DataViz.Rmd",
+            "04-Reproducibility.Rmd",
+            "05-Sharing.Rmd",
             "About.Rmd",
             "References.Rmd"]
 new_session: yes

_output.yml

@@ -1,16 +1,18 @@
 bookdown::gitbook:
-  css: assets/style.css
+  css: assets/style_ITN.css
   includes:
-    before_body: assets/big-image.html
-    after_body: [assets/footer.html, assets/open-new-tab.html]
-    highlight: tango
+    before_body: assets/big-image-itcr.html
+    after_body: assets/footer.html
+  highlight: tango
   config:
     toc:
       collapse: section
       before: |
-       <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
+       <a href="https://www.itcrtraining.org/"><img src="assets/ITN_logo.png" style="padding-left: 15px; padding-top: 8px;"</a>
       after: |
        <p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
        <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
        <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
+       <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span>  <a href="https://forms.gle/hc8Xt3Y2Znjb6M4Y7"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>

assets/big-image-itcr.html

@@ -0,0 +1,12 @@
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=1.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+  <link href="assets/style_ITN.css" rel="stylesheet">
+</head>
+
+
+
+<div class="hero-image-container"> 
+  <img class= "hero-image" src="assets/itcr_main_image.png">
+</div>