diff --git a/.gitignore b/.gitignore index f9f1d49..02879cf 100644 --- 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 index b4d0f13..c7905b0 100644 --- 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! \ No newline at end of file diff --git a/docs/Dry Lab SOPs/Basics.md b/docs/Dry Lab SOPs/Basics.md index 1395be7..9b71df0 100644 --- 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 \ No newline at end of file +## Uploading Our Raw Data for Review \ No newline at end of file diff --git a/docs/Dry Lab SOPs/Single-Cell_ATACseq.md b/docs/Dry Lab SOPs/Single-Cell_ATACseq.md index 57b0128..2ce5f96 100644 --- 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 \ No newline at end of file +## Starting from Public Summary Statistics \ No newline at end of file diff --git a/docs/Dry Lab SOPs/Single-Cell_RNAseq.md b/docs/Dry Lab SOPs/Single-Cell_RNAseq.md index dd0c705..d0d78b8 100644 --- 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 \ No newline at end of file +## Starting from Public Summary Statistics \ No newline at end of file diff --git a/docs/Dry Lab SOPs/Spatial_RNAseq.md b/docs/Dry Lab SOPs/Spatial_RNAseq.md index e5647dd..67ef108 100644 --- 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 \ No newline at end of file +## Starting from Public Summary Statistics \ No newline at end of file diff --git a/docs/Dry Lab SOPs/index.md b/docs/Dry Lab SOPs/index.md index 41690fd..d816a5d 100644 --- 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. \ No newline at end of file diff --git a/docs/Intro to Computation/Bioinformatics.md b/docs/Intro to Computation/Bioinformatics.md new file mode 100644 index 0000000..bf0b06e --- /dev/null +++ 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 new file mode 100644 index 0000000..cab4456 --- /dev/null +++ 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 new file mode 100644 index 0000000..0d78970 --- /dev/null +++ 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 new file mode 100644 index 0000000..37e5a57 --- /dev/null +++ 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 index 28935f5..2b8b8e6 100644 --- 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 index f891f3d..8cb9d39 100644 --- 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 index c37dc2f..e907f93 100644 --- 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 new file mode 100644 index 0000000..40faba8 --- /dev/null +++ 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 new file mode 100644 index 0000000..7cbc133 --- /dev/null +++ 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 new file mode 100644 index 0000000..7c9a64f --- /dev/null +++ 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 new file mode 100644 index 0000000..f49fa1b --- /dev/null +++ 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 index 1c7c9d8..24d933d 100644 --- 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. \ No newline at end of file diff --git a/docs/Wet Lab SOPs/index.md b/docs/Wet Lab SOPs/index.md index de8381e..2ae6178 100644 --- 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 index 874b786..a13e698 100644 --- 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). \ No newline at end of file