White Lab Protocols

This repository contains notes and protocols for mass spectrometry analysis of proteomes. For an introduction to our lab's proteomics workflow, check the mass_spec folder, and for other protocols, check the protocols and cell_culture folders.

PDF Documents

We supply automatically-compiled PDFs of tagged commits on our releases page:

• All Protocols : All protocols currently used in the lab.
• Proteomics Protocols : A series of protocols to prepare sample lysates for proteomics analysis.
• Wet Lab Protocols : Various protocols for cloning and molecular biology analysis.
• Cell Culture Protocols : Protocols for cell culture.
• Legacy Protocols : Old protocols that have been deprecated or combined into newer workflows.

Lab Parts and Reagents

We keep a catalog of our commonly ordered lab supplies in this repository's parts folder:

• HPLC Parts
• Wet Lab

Development

All documents contained here are written using Markdown.

To edit these documents, you will need to be added to the White-Lab GitHub group. Then you can either use GitHub's in-browser editor to create and update files or you can clone the repository to edit files locally.

To generate a final release, you will need to tag the latest release locally, and then push the tag to GitHub:

git tag -a 2019-07-01 -m "Added protocols with alternate cell lysis methods."
git push --tags

Building Releases

Our PDFs are build on tagged releases using Travis-CI. To build the PDFs yourself, install md-to-pdf via the node package manager and run make:

# On CentOS / Fedora / RHEL
sudo yum install npm

# On Debian / Ubuntu
sudo apt-get install npm

# Other environments: https://nodejs.org/en/download/

npm install -g md-to-pdf
make

See .travis.yml for an example build environment.