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
- 7-fit-functions.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
1 maintainer
Metadata
1 maintainer
Release files for dinkum-bio 0.6.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| dinkum_bio-0.6.1.tar.gz | 38.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| dinkum_bio-0.6.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 80.4 kB
Release files / dinkum_bio-0.6.1.tar.gz
| Download URL | dinkum_bio-0.6.1.tar.gz |
|---|---|
| Size | 38.0 kB |
| Tags | Source |
|
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twine/6.0.1 CPython/3.11.8
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Release files / dinkum_bio-0.6.1-py3-none-any.whl
| Download URL | dinkum_bio-0.6.1-py3-none-any.whl |
|---|---|
| Size | 42.5 kB |
| Tags | Python 3 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.0.1 CPython/3.11.8
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