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https://github.com/filipinascimento/bl-network-preprocess
App to preprocess connectivity/similarity matrices (conmat) and generate a filtered version of the network, which can be directed or undirected, weighted or unweighted.
https://github.com/filipinascimento/bl-network-preprocess
network
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App to preprocess connectivity/similarity matrices (conmat) and generate a filtered version of the network, which can be directed or undirected, weighted or unweighted.
- Host: GitHub
- URL: https://github.com/filipinascimento/bl-network-preprocess
- Owner: filipinascimento
- License: mit
- Created: 2020-03-22T04:02:42.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2020-10-15T18:11:49.000Z (over 4 years ago)
- Last Synced: 2024-11-08T06:26:52.513Z (3 months ago)
- Topics: network
- Language: Python
- Homepage:
- Size: 729 KB
- Stars: 0
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
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.289)
# Network Preprocess
App to preprocess networks and generate a filtered version of it, which can be directed or undirected, weighted or unweighted.
### 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)
## Running the App
### On Brainlife.io
You can submit this App online at [https://doi.org/10.25663/brainlife.app.289](https://doi.org/10.25663/brainlife.app.289) 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
```
The `filsilva/cxnetwork` ( [https://github.com/filipinascimento/cxnetworks-docker](https://github.com/filipinascimento/cxnetworks-docker) ) docker image is being used.
### Sample Datasets
A sample dataset is provided in folder `data` and `config-sample.json`
## Output
The output is a preprocessed `network` data type.
### 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
```