thejacksonlaboratory / geneweaver-docs

Documentation site for the Geneweaver project.

Geneweaver Documentation

This repository contains the central documentation site for the GeneWeaver project. Geneweaver is a web-based software tool for the integration of functional genomics data. The Geneweaver web application is available at Geneweaver.org.

The documentation is built using MkDocs and Material for MkDocs, and is hosted on GitHub Pages.

You can view the documentation at https://thejacksonlaboratory.github.io/geneweaver-docs/.

Getting Started

First, clone this repository to your local machine:

git clone [email protected]:TheJacksonLaboratory/geneweaver-docs.git
cd geneweaver-docs

To view the documentation locally, you will need to have MkDocs installed on your machine. If you don't have it already, you can install it using poetry, or with pip:

Using Poetry

poetry install

Using Pip

pip install mkdocs

Once you have MkDocs installed, you can view the documentation by running the following command:

mkdocs serve

This will start a local development server at http://localhost:8000/, where you can view the documentation in your web browser.

Contributing

If you notice any errors or omissions in the documentation, please feel free to submit a pull request with your changes. We welcome contributions from the community!

geneweaver-docs's Issues

Improve the wording of the Species section on the reference/data-model page.

The wording of "Genesets are of a species, that is, the genomic features in the geneset are from a specific species" is a bit odd, and could use improvement to make it a) more understandable, and b) more specific.

Automate the Github Pages deployment

We should use CICD to automate deploying to GitHub Pages.

Make sure pip/poetry usage is consistent throughout the site.

The preferred pattern is to use the tabs, for example:

=== "Poetry"
    ```console
    $ poetry add geneweaver-tools
    ```
=== "Pip"
    ```console
    $ pip install geneweaver-tools
    ```

"Integration and Aggregation" Tutorial

A Python Jupyter Notebook style tutorial would be a helpful addition to the documentation. It would provide an accessible entrypoint to understanding how Geneweaver can be used as a research discovery tool.

For example, this Tensorflow tutorial is a good reference: https://www.tensorflow.org/tutorials/images/data_augmentation.

We should start with a high level summary of what the tutorial will accomplish, and then develop an outline of the steps that will be included in the tutorial. After that we can implement the tutorial in a python Jupyter notebook.

Unfinished tutorial sections should include a brief overview future content

Each page without content should at least include a a description of what the content will do once finished.

Broken link on Genes and Genesets page

The link in the admonition on the bottom of this page is broken: https://bergsalex.github.io/geneweaver-docs/concepts/genes-and-genesets/.

It should send the user here: https://bergsalex.github.io/geneweaver-docs/reference/geneset-tiers/