Added: Jekyll with 'Just the Docs' template with sidebar navigation

0_intro/0_intro.md

@@ -1,3 +1,9 @@
+---
+title: 0. Introduction
+layout: default
+nav_enabled: true
+---
+
 # Introduction to the DBTL Bootcamp
 [Introduction](/0_intro/0_intro.md) >> [Design](/1_design/1_design.md) >> [Build](/2_build/2_build.md) >> [Test](/3_test/3_test.md) >> [Learn](/4_learn/4_learn.md)
 
@@ -13,6 +19,10 @@ They ask how might you actually test the components of your design, what expecta
 > All of these questions might be a bit disheartening, but they are important ones, and there are so many tools and resources available to address these challenges. 
 And the Design > Build > Test > Learn (DBTL) cycle can help you address these in a systematic way.
 
+
+![DBTL cycle](assets/images/iGEM-DBTL-cycle.png)
+*The DBTL cycle*
+
 <figure>
 <center>
 <img src="assets/images/iGEM-DBTL-cycle.png" width=30% />
@@ -95,6 +105,9 @@ We do recommend starting with the [Design Module](/1_design/1_design.md) though!
 
 ### What exactly am I designing/building/testing/learning?
 
+![TU](assets/images/transcription-unit-labeled.png)
+*A simplified diagram of the kind of transcription units you will build: promoter, ribosome binding site (rbs), coding sequence (cds), terminator, in a plasmid backbone.*
+
 <center>
 <figure>
 <img src="assets/images/transcription-unit-labeled.png" width=50% />
@@ -355,4 +368,4 @@ In visual representations these are usually not included, but we have provided t
 
 Finally, Golden Gate Assembly is an extremely powerful assembly technique and can be made more complex with when an GGA-based assembly standard supports hierarchical assemblies, where you would be able to assemble multiple transcription units to create larger genetic circuits. 
 This may be a consideration for your own project which you will need to include in your Design process. 
-But for this bootcamp, all you will need to be prepared for is the above!
+But for this bootcamp, all you will need to be prepared for is the above!

1_design/1_design.md

@@ -1,3 +1,9 @@
+---
+title: 1. Design Module
+layout: default
+nav_enabled: true
+---
+
 # Design Module
 [Introduction](/0_intro/0_intro.md) >> [Design](/1_design/1_design.md) >> [Build](/2_build/2_build.md) >> [Test](/3_test/3_test.md) >> [Learn](/4_learn/4_learn.md)
 

2_build/2_build.md

@@ -1,3 +1,9 @@
+---
+title: 2. Build Module
+layout: default
+nav_enabled: true
+---
+
 # Build Module
 [Introduction](/0_intro/0_intro.md) >> [Design](/1_design/1_design.md) >> [Build](/2_build/2_build.md) >> [Test](/3_test/3_test.md) >> [Learn](/4_learn/4_learn.md)
 

3_test/3_test.md

@@ -1,3 +1,9 @@
+---
+title: 3. Test Module
+layout: default
+nav_enabled: true
+---
+
 # Test Module
 
 **The Test Module is currently under development.**

4_learn/4_learn.md

@@ -1,3 +1,8 @@
+---
+title: 4. Learn
+layout: default
+nav_enabled: true
+---
 <script type="text/javascript" async
   src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/MathJax.js?config=TeX-MML-AM_CHTML">
 </script>
@@ -12,7 +17,7 @@
 
 ## Mathematical Expressions
 
-Inline math: $E = mc^2$
+Inline math: $$E = mc^2$$
 
 Block math:
 $$
@@ -21,7 +26,7 @@ $$
 
 
 
-The equation $3x^2 + 5x +1 = 0$ has the solutions
+The equation $$3x^2 + 5x +1 = 0$$ has the solutions
 
 $$
 x_{1,2} = \frac{-5 \pm \sqrt{5^2-12}}{6}

Gemfile

@@ -0,0 +1,7 @@
+source 'https://rubygems.org'
+
+gem "jekyll", "~> 4.4.1" # installed by `gem jekyll`
+# gem "webrick"        # required when using Ruby >= 3 and Jekyll <= 4.2.2
+
+gem "just-the-docs", "0.10.1" # pinned to the current release
+# gem "just-the-docs"        # always download the latest release

README.md

@@ -1,5 +1,3 @@
-*Disclaimer: This bootcamp is designed to provide participants with valuable skills and knowledge in engineering biology. However, completion of the bootcamp does not guarantee job placement, salary increases, or career advancement. We do not offer refunds once the bootcamp has commenced. Participants are responsible for their own job search and career development efforts. While we strive to provide accurate and up-to-date information, we are not responsible for errors or omissions. The curriculum and instructors are subject to change without notice.*
-
 # The iGEM Engineering DBTL Bootcamp
 
 The **D**esign-**B**uild-**T**est-**L**earn (DBTL) Bootcamp is an open-source bootcamp in development by the [iGEM Engineering Committee](https://technology.igem.org/engineering-committee). 
@@ -17,17 +15,10 @@ They may also have additional supplementary documentation, folders, assets, and
 
 This github repository contains documentation, assets, and files for the bootcamp, however, several external resources and tools are linked to, referenced, and/or recommended.
 
-0. [Introduction](./0_intro/0_intro.md)
-1. [Design](./1_design/1_design.md)
-2. [Build](./2_build/2_build.md)
-3. [Test](./3_test/3_test.md)
-4. [Learn](./4_learn/4_learn.md)
-
 ## Contributing
 Currently, only iGEM Engineering Committee members can contribute to the DBTL Bootcamp. 
 
 In the future, we would like to encourage external contributors to help maintain and improve this documentation! 
 But for now, if you would like to contribute, please join the [iGEM Engineering Committee](https://technology.igem.org/engineering-committee).
 
-If you would like to adapt this bootcamp, please refer to the [license](/LICENSE).
-
+If you would like to adapt this bootcamp, please refer to the [license](/LICENSE).

_config.yml

@@ -1,3 +1,17 @@
-#theme: minima
-# Conversion
-#markdown: kramdown
+title: iGEM DBTL Bootcamp
+description: The Design-Build-Test-Learn (DBTL) Bootcamp goal  is to help teams familiarize themselves with the DBTL cycle for engineering biological systems
+
+theme: just-the-docs
+
+url: https://igem-engineering.github.io/iGEM-DBTL-bootcamp/
+
+favicon_ico: "/assets/images/favicon.ico"
+
+aux_links:
+  iGEM Technology: https://technology.igem.org
+
+callouts:
+  warning:
+    title: Warning
+    color: red
+

index.md

@@ -0,0 +1,36 @@
+---
+title: Home
+layout: home
+---
+{: .d-inline-block }
+
+
+{: .warning }
+
+> **Disclaimer**: This bootcamp is designed to provide participants with valuable skills and knowledge in engineering biology. However, completion of the bootcamp does not guarantee job placement, salary increases, or career advancement. We do not offer refunds once the bootcamp has commenced. Participants are responsible for their own job search and career development efforts. While we strive to provide accurate and up-to-date information, we are not responsible for errors or omissions. The curriculum and instructors are subject to change without notice.
+
+# The iGEM Engineering DBTL Bootcamp
+
+The **D**esign-**B**uild-**T**est-**L**earn (DBTL) Bootcamp is an open-source bootcamp in development by the [iGEM Engineering Committee](https://technology.igem.org/engineering-committee). 
+
+The goal of the bootcamp is to help teams familiarize themselves with the [DBTL cycle for engineering biological systems](https://technology.igem.org/engineering/introduction). 
+Specifically, it has teams designing, building, testing, and analyzing characterization data for green fluorescent protein (GFP) reporter constructs of varying promoter strength.
+
+While this is only a brief introduction to designing and building genetic circuits, and team projects are far more complex, we hope that some of the approaches and tools used in the bootcamp can be applied to any project. 
+
+## Structure
+The DBTL Bootcamp is divided into an Introduction, four "Modules" (each covering its namesake stage in the DBTL cycle), and a folder for part/plasmid files.
+Each module has its own folder and introductory document. 
+They may also have additional supplementary documentation, folders, assets, and files that are specific to that module.
+
+
+This github repository contains documentation, assets, and files for the bootcamp, however, several external resources and tools are linked to, referenced, and/or recommended.
+
+
+## Contributing
+Currently, only iGEM Engineering Committee members can contribute to the DBTL Bootcamp. 
+
+In the future, we would like to encourage external contributors to help maintain and improve this documentation! 
+But for now, if you would like to contribute, please join the [iGEM Engineering Committee](https://technology.igem.org/engineering-committee).
+
+If you would like to adapt this bootcamp, please refer to the [license](/LICENSE).