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Use '# page.title' to reduce chances of mistakes. Downside, all headers in the file itself now have to be ##. Added some pages. Added Gemfile.lock to the .gitignore since testing usually requires a different version, but the committed one works with github.
yuyanchenglab · Jul 11, 2024 · 67ee96b · 67ee96b
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diff --git a/.gitignore b/.gitignore
@@ -13,3 +13,5 @@ _site/
 # Ignore folders generated by Bundler
 .bundle/
 vendor/
+
+Gemfile.lock
diff --git a/docs/Completed Projects/index.md b/docs/Completed Projects/index.md
@@ -5,6 +5,6 @@ has_children: true
 nav_order: 8
 ---
 
-# Completed Projects
+# {{page.title}}
 
 Below are some of the projects that our lab would like you to admire and whose success we want you to match!
diff --git a/docs/Dry Lab SOPs/Basics.md b/docs/Dry Lab SOPs/Basics.md
@@ -3,13 +3,15 @@ layout: default
 title: Basics
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 0
+nav_order: 1
 ---
 
-# Overview of how to use PMACS
+# {{page.title}}
+
+## Overview of how to use PMACS
 
 Refer to Wiki and Bala
 
-# The different types of analyses that we do
+## The different types of analyses that we do
 
-# Uploading Our Raw Data for Review
+## Uploading Our Raw Data for Review
diff --git a/docs/Dry Lab SOPs/Single-Cell_ATACseq.md b/docs/Dry Lab SOPs/Single-Cell_ATACseq.md
@@ -3,13 +3,13 @@ layout: default
 title: Single-Cell ATACseq
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 3
+nav_order: 2
 ---
 
-# Overview of Github 
+# {{page.title}}
 
-# Data Sources
+## Data Sources
 
-# Starting from Public or Private Fastq Files
+## Starting from Public or Private Fastq Files
 
-# Starting from Public Summary Statistics
+## Starting from Public Summary Statistics
diff --git a/docs/Dry Lab SOPs/Single-Cell_RNAseq.md b/docs/Dry Lab SOPs/Single-Cell_RNAseq.md
@@ -3,13 +3,13 @@ layout: default
 title: Single-Cell RNAseq
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 2
+nav_order: 1
 ---
 
-# Overview of Github 
+# {{page.title}}
 
-# Data Sources
+## Data Sources
 
-# Starting from Public or Private Fastq Files
+## Starting from Public or Private Fastq Files
 
-# Starting from Public Summary Statistics
+## Starting from Public Summary Statistics
diff --git a/docs/Dry Lab SOPs/Spatial_RNAseq.md b/docs/Dry Lab SOPs/Spatial_RNAseq.md
@@ -3,13 +3,13 @@ layout: default
 title: Spatial RNAseq
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 1
+nav_order: 3
 ---
 
-# Overview of Github 
+# {{page.title}}
 
-# Data Sources
+## Data Sources
 
-# Starting from Public or Private Fastq Files
+## Starting from Public or Private Fastq Files
 
-# Starting from Public Summary Statistics
+## Starting from Public Summary Statistics
diff --git a/docs/Dry Lab SOPs/index.md b/docs/Dry Lab SOPs/index.md
@@ -5,6 +5,6 @@ has_children: true
 nav_order: 7
 ---
 
-# Dry Lab SOPs
+# {{page.title}}
 
 These are the procedures that our computation team in the lab uses for reference and reproducibility.
diff --git a/docs/Intro to Computation/Bioinformatics.md b/docs/Intro to Computation/Bioinformatics.md
@@ -0,0 +1,17 @@
+---
+layout: default
+title: Intro to Bioinformatics
+nav_order: 4
+parent: Intro to Computation
+has_children: false
+---
+
+# {{page.title}}
+
+Here is where we can overlap with the biology team.
+
+## Why?
+
+## Central Dogma
+
+## Pairing Desired Information with Data Type
diff --git a/docs/Intro to Computation/ComputationResourses.md b/docs/Intro to Computation/ComputationResourses.md
@@ -0,0 +1,13 @@
+---
+layout: default
+title: Intro to Computational Resources
+nav_order: 1
+parent: Intro to Computation
+has_children: false
+---
+
+# {{page.title}}
+
+## PMACS Access
+
+## PMACS etiquette
diff --git a/docs/Intro to Computation/Programming.md b/docs/Intro to Computation/Programming.md
@@ -0,0 +1,15 @@
+---
+layout: default
+title: Intro to Programming
+nav_order: 2
+parent: Intro to Computation
+has_children: false
+---
+
+# {{page.title}}
+
+## Intro to the Command Line
+
+## Intro to Python
+
+## Intro to R
diff --git a/docs/Intro to Computation/SourceControl.md b/docs/Intro to Computation/SourceControl.md
@@ -0,0 +1,15 @@
+---
+layout: default
+title: Source Control
+nav_order: 3
+parent: Intro to Computation
+has_children: false
+---
+
+# {{page.title}}
+
+## Intro to Git
+
+## Github Usage
+
+## Intro to Virtual Environments
diff --git a/docs/Intro to Computation/index.md b/docs/Intro to Computation/index.md
@@ -1,28 +1,8 @@
 ---
 layout: default
 title: Intro to Computation
-has_children: false
+has_children: true
 nav_order: 3
 ---
 
-# Intro to Computation
-
-## PMACS Access
-
-## PMACS etiquette
-
-## Github Usage
-
-## Intro to the Command Line
-
-## Intro to Python
-
-## Intro to R
-
-## Intro to Git
-
-## Intro to Virtual Environments
-
-## Introduction to Bioinformatics
-
-Here is where we can overlap with the biology team.
+# {{page.title}}
diff --git a/docs/Intro to the Biology Lab/index.md b/docs/Intro to the Biology Lab/index.md
@@ -5,7 +5,7 @@ has_children: false
 nav_order: 4
 ---
 
-# Intro to the Biology Lab
+# {{page.title}}
 
 ## How to clean the lab to avoid data contamination
 

diff --git a/docs/Lab Resources/index.md b/docs/Lab Resources/index.md
@@ -5,7 +5,7 @@ has_children: false
 nav_order: 5
 ---
 
-# Lab Resources
+# {{page.title}}
 
 ## Penn Resources in General
 
@@ -15,6 +15,8 @@ nav_order: 5
 
 ## Technical Support
 
+## Our Neighbors in Stellar-Chance
+
 ## This Website
 
 This website is a [github-pages](https://docs.github.com/en/pages) site using [just-the-docs](https://open.win.ox.ac.uk/pages/open-science/community/just-the-docs-v040/) and [jekyll](https://jekyllrb.com/docs/) to get it running.

diff --git a/docs/Onboarding/DryLabTraining.md b/docs/Onboarding/DryLabTraining.md
@@ -0,0 +1,15 @@
+---
+layout: default
+title: Dry Lab Training
+nav_order: 4
+parent: Onboarding
+has_children: false
+---
+
+# {{page.title}}
+
+## General
+
+## Staff
+
+## Students
diff --git a/docs/Onboarding/LabAccess.md b/docs/Onboarding/LabAccess.md
@@ -0,0 +1,27 @@
+---
+layout: default
+title: Lab Access
+nav_order: 2
+parent: Onboarding
+has_children: false
+---
+
+# {{page.title}}
+
+## Building, Lab and Facility
+
+Access to Stellar-Chance and BRB
+
+Stellar-Chance 310 and offices
+
+## Penn Medicine Email
+
+## PMACS Account for Compute
+
+## Lab Communication
+
+slack, trello, google, labarxiv...
+
+## Printers and Other Equipment
+
+## Contact Info
diff --git a/docs/Onboarding/Prerequisites.md b/docs/Onboarding/Prerequisites.md
@@ -0,0 +1,17 @@
+---
+layout: default
+title: Prerequisites
+nav_order: 1
+parent: Onboarding
+has_children: false
+---
+
+# {{page.title}}
+
+## Permanent Staff
+
+## Temporary Staff
+
+## Postdocs
+
+## Students
diff --git a/docs/Onboarding/WetLabTraining.md b/docs/Onboarding/WetLabTraining.md
@@ -0,0 +1,18 @@
+---
+layout: default
+title: Wet Lab Training
+nav_order: 3
+parent: Onboarding
+has_children: false
+---
+
+# {{page.title}}
+
+## General
+
+### Handling package Deliveries
+
+## Staff
+
+## Students
+
diff --git a/docs/Onboarding/index.md b/docs/Onboarding/index.md
@@ -5,21 +5,6 @@ has_children: true
 nav_order: 2
 ---
 
-# Onboarding
-
-## Pre-Requisites
-
-HIPAA, training on workday
-
-## Access to Stellar-Chance and BRB
-
-## Handling package Deliveries
-
-## Our Spaces
-
-Stellar-Chance 310 and offices
-
-## Our Neighbors and co-workers in Stellar-Chance
-
-## Other
+# {{page.title}}
 
+Welcome to the lab! You will find here some resources to get started with us.
diff --git a/docs/Wet Lab SOPs/index.md b/docs/Wet Lab SOPs/index.md
@@ -1,11 +1,11 @@
 ---
 layout: default
 title: Wet Lab SOPs
-has_children: false
+has_children: true
 nav_order: 6
 ---
 
-# Wet Lab SOPs
+# {{page.title}}
 
 Here we document the procedure to perform certain techniques in the wet lab.
 

diff --git a/index.md b/index.md
@@ -8,6 +8,6 @@ permalink: /
 
 # Welcome to the Cheng Molecular Opthalmology lab!
 
-This is the internal website for the Cheng Molecular Opthalmology lab's onboarding and a repository for Standard Operating Procedures (SOP).
+This is the internal website for the Cheng Molecular Opthalmology lab's onboarding and a repository for our Standard Operating Procedures (SOP).
 
 This documentation website was created using [Jekyll and Github pages](https://help.github.com/en/github/working-with-github-pages/setting-up-a-github-pages-site-with-jekyll).