Skip to content

Lab Docs

This resource provides documentation for general wet lab and dry lab organization and pipelines for the Zamanian Lab at the University of Wisconsin-Madison. This is an evolving resource.

How to Use this Guide

New lab members should first orient themselves with our Lab Manual and Computational Guide documents. Many finalized lab protocols are maintained on the Protocols page. Pipelines provides detailed information on local and server-based computational pipelines. Lab GDrive provides links to Google docs and sheets that are maintained by the laboratory.

Updating

This resource is by nature an open, living, and collaborative document. We are using MkDocs as our site generator which uses a simply structured GitHub repository that includes Markdown files as the documentation and a few ancillary files to help in generation. You will need to have your own GitHub account and will need to be a member of the @zamanianlab organization in order to gain editing privileges. To edit this document, please follow the instructions below.

  1. Install MkDocs and the Material theme in a conda environment

    conda create --name labdocs python=3.9
    conda activate labdocs
    pip install mkdocs
    pip install mkdocs-material
    

  2. Clone the ZamanianLabDocs repo:

    git clone https://github.com/zamanianlab/ZamanianLabDocs.git

  3. Create and edit a Markdown file (save in /docs/ with the .md extension).

    NOTE: if adding/editing a protocol, make a new folder /docs/protocols titled {protocol_name}. If adding images, make a new folder called img in /docs/protocols/{protocol_name}

  4. Push to GitHub

  5. Build and deploy site

    mkdocs build && mkdocs gh-deploy

  6. Optional: before deploying with gh-deploy, view the site locally with mkdocs serve

  7. After deploying, check to ensure everything deployed as expected by visiting https://www.zamanianlab.org/ZamanianLabDocs/