dinkum-bio 0.6.0

directed interaction network kit for modeling, focused on GRNs

dinkum

Directed Interaction NetworKs are fair dinkum!

What is dinkum?

dinkum is a piece of software for simple modeling of gene regulatory networks, initially based on the GeNeTool software described in Faure, Peter, and Davidson, 2013. It supports simple definition of genes, tissues, ligands/receptors, and regulatory influences, and is intended to run in Jupyter Notebooks. It's primarily intended for teaching purposes, and was developed for the 2024 Gene Regulatory Networks for Development course at the Marine Biological Laboratory.

To get started with dinkum, see notebooks/0-getting-started.ipynb. Here is a full list of example Jupyter notebooks:

• 0-getting-started.ipynb
• 1-positive-feedback.ipynb
• 2-simple-oscillation.ipynb
• 4-double-negative-gate.ipynb
• 5-intermediate-custom-logic.ipynb
• 6-decay-example.ipynb
• 6-multi-level-activation.ipynb
• 9-advanced-examples.ipynb

Why 'dinkum'?

Dinkum is a backronym constructed from "directed interaction networks". It's also named in honor of one of the course directors, who is Australian; it turns out that dinkum is one of the few Australian-specific slang words that is not rude.

Installing dinkum

dinkum is available on the Python Package Index, PyPI, as dinkum-bio. It requires Python 3.11 or later.

To install:

pip install dinkum-bio

Developing dinkum

Dinkum is developed on github under dinkum-bio/dinkum. It is released under the GNU Affero General Public License v3 open source license.

You can run the tests with make test.

CTB 10/2024