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https://github.com/filipinascimento/bl-network-measurements
App to calculate several basic statistics for networks and their respective null model distributions.
https://github.com/filipinascimento/bl-network-measurements
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App to calculate several basic statistics for networks and their respective null model distributions.
- Host: GitHub
- URL: https://github.com/filipinascimento/bl-network-measurements
- Owner: filipinascimento
- License: mit
- Created: 2020-02-24T17:02:54.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2023-04-26T19:39:30.000Z (almost 2 years ago)
- Last Synced: 2024-11-08T06:26:43.482Z (3 months ago)
- Topics: network
- Language: Python
- Homepage:
- Size: 2.72 MB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://github.com/brain-life/abcd-spec)
[](https://doi.org/10.25663/brainlife.app.321)
# Network Measurements
App to calculate several basic statistics for networks and their respective null model distributions.
## List of measurements:
### Node-based measurements:
- *Degree*
- *In-Degree* (`directed`)
- *Out-Degree* (`directed`)
- *Strength* (`weighted`)
- *In-Strength* (`directed`,`weighted`)
- *Out-Strength* (`directed`,`weighted`)
- *Clustering* Coefficient
- *Coreness*
- *Match Index*
- *Betweeness Centrality*
- *Betweeness CentralityWeighted* (`weighted`)
### Network-based measurements:
- *Avg. Degree*
- *Avg. In-Degree* (`directed`)
- *Avg. Out-Degree* (`directed`)
- *Avg. Strength* (`weighted`)
- *Avg. In-Strength* (`directed`,`weighted`)
- *Avg. Out-Strength* (`directed`,`weighted`)
- *Avg. Clustering* Coefficient
- *Betweenness Centralization*
- *Rich-Club Coefficient*
- *Degree Assortativity*
- *Diameter*
- *Module Degree Z-Score* (`communities`)
- *Participation Coefficient* (`communities`)
- *Modularity* (`communities`)
> TODO: Add references for all statistics
Some statistics are calculated only for `directed` or `weighted` networks. Those requiring `communities` are only calculated if the Communities App was executed on this data before.
### Authors
- [Filipi N. Silva](https://filipinascimento.github.io)
### Contributors
- [Franco Pestilli](https://liberalarts.utexas.edu/psychology/faculty/fp4834)
### Funding Acknowledgement
brainlife.io is publicly funded and for the sustainability of the project it is helpful to Acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your publications and code reusing this code.
[](https://nsf.gov/awardsearch/showAward?AWD_ID=1734853)
[](https://nsf.gov/awardsearch/showAward?AWD_ID=1636893)
[](https://nsf.gov/awardsearch/showAward?AWD_ID=1916518)
[](https://nsf.gov/awardsearch/showAward?AWD_ID=1912270)
[](https://grantome.com/grant/NIH/R01-EB029272-01)
### Citations
1. Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). [https://doi.org/10.1038/s41597-019-0073-y](https://doi.org/10.1038/s41597-019-0073-y)
2. Bassett, Danielle S., and Olaf Sporns. "Network neuroscience." Nature neuroscience 20, no. 3 (2017): 353. [https://doi.org/10.1038/nn.4502](https://doi.org/10.1038/nn.4502)
3. Costa, L. da F., Francisco A. Rodrigues, Gonzalo Travieso, and Paulino Ribeiro Villas Boas. "Characterization of complex networks: A survey of measurements." Advances in physics 56, no. 1 (2007): 167-242.[https://doi.org/10.1080/00018730601170527](https://doi.org/10.1080/00018730601170527)
## Running the App
### On Brainlife.io
You can submit this App online at [https://doi.org/10.25663/brainlife.app.321](https://doi.org/10.25663/brainlife.app.321) via the "Execute" tab.
### Running Locally (on your machine)
Singularity is required to run the package locally.
1. git clone this repo.
```bash
git clone
cd
```
2. Inside the cloned directory, edit `config-sample.json` with your data or use the provided data.
3. Rename `config-sample.json` to `config.json` .
```bash
mv config-sample.json config.json
```
4. Launch the App by executing `main`
```bash
./main
```
### Sample Datasets
A sample dataset is provided in folder `data` and `config-sample.json`
## Output
The output is a `network` enriched with the measurements. You can use Network Visualization and Network Report to generate visualizations, plots and tables of the results.
### Dependencies
This App only requires [singularity](https://www.sylabs.io/singularity/) to run. If you don't have singularity, you will need to install the python packages defined in `environment.yml`, then you can run the code directly from python using:
```bash
./main.py config.json
```