Metadata-Version: 2.1
Name: cxsystem2
Version: 0.0a4
Summary: A cerebral cortex simulation framework
Home-page: https://github.com/VisualNeuroscience-UH/CxSystem2
Author: Vafa Andalibi, Henri Hokkanen, Simo Vanni
Author-email: vafa.andalibi@gmail.com
License: GPL v3.0
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Win32 (MS Windows)
Classifier: Environment :: MacOS X
Classifier: Environment :: X11 Applications
Classifier: Environment :: Console
Classifier: Intended Audience :: Information Technology
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Utilities
Description-Content-Type: text/markdown
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<a href="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/README.md"><img src="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/data_config/icon/cxsystem_logo.png?sanitize=true" width="60%"></a>

# CxSystem2, A Flexible Cortical Simulation Framework
> Warning: CxSystem2 GUI is developed for using in a local environment and should not be installed on a publicly accessible server unless extra security measures are added on top of it  

[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/LICENSE) 
[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/bug.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Abug)
[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/enhancement.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Aenhancement)
[![Github Issues](http://img.shields.io/github/issues-pr/VisualNeuroscience-UH/CxSystem2.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/pulls)
[![Documentation Status](https://readthedocs.org/projects/cxsystem/badge/?version=master)](http://cxsystem.readthedocs.io/en/master/?badge=master)

## Table of Contents 

- [Synopsis](#synopsis)
- [Installation](#installation)
    * [Windows](#windows)
    * [Linux/Mac](#linuxmac)
    * [Development](#development)
- [Interfaces]
    * [Browser User Interface (BUI)](#bui)
    * [Terminal Commands](#commands)
- [Citation](#Citation)
- [Support](#support)
- [Team](#team)
- [License](#license)

## Synopsis

CxSystem is a cerebral cortex simulation framework, which operates on personal computers. We have tested the simulation software with a simplified version of a comprehensive cortical microcircuit model [1], which is available as configuration file. 

The CxSystem aims at easy testing and buildup of diverse models at single cell resolution.  Implemented on the top of the Python-based [Brian2 simulator](https://github.com/brian-team/brian2), CxSystem supports the main goal of Brian, i.e. minimizing development time, by providing the user with a simplified interface.

The preliminary version of this software has been developed at Aalto University 2012-2015 [2], and the full version at the University of Helsinki 2013-2017. The software is distributed under the terms of the GNU General Public License, Copyright 2017 Vafa Andalibi, Henri Hokkanen and Simo Vanni.

To access the documentation of the CxSystem, please check out the [readthedocs page](http://cxsystem.readthedocs.io/en/master/) of the project.

## Installation

We highly recommend installing `CxSystem2` on a virtual environment. Use the following commands to install a Python3 virtual environment and install CxSystem: 

### Windows

 Make sure you have python 3.5 or above. To create activate a `venv` in windows at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command): 

```shell
C:\> python --version
Python 3.7.4
C:\> python3 -m venv %userprofile%\CX2
C:\> %userprofile%\CX2\Scripts\activate
(CX2) C:\> pip install cxsystem2
```

### Linux/Mac

Make sure you have python 3.5 or above. To create activate a `venv` in Linux/Mac at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command): 

```shell
$ python --version
Python 3.7.4
$ python3 -m venv ~/CX2
$ source ~/CX2/bin/activate
$ pip install cxsystem2 
(CX2) user@DESKTOP:~$ pip install cxsystem2
```

### Development

To develop `CxSystem2`, after creating the repository install it with the following commands: 

```shell
(CX2) $ git clone https://github.com/VisualNeuroscience-UH/CxSystem2
(CX2) $ cd CxSystem2
(CX2) $ pip install -r requirements.txt
(CX2) $ pip install -e . 
```

With this method any change to the code will be reflected on the package immediately. 

## Interfaces

`CxSystem2` comes with two interfaces:

### Browser User Interface (BUI)

CxSystem's BUI is built to provide users with an interactive environment for changing the parameters for simulations. 

### Terminal Commands

Beside the BUI, Some of the main functionalities of the `CxSystem2` are available as terminal Commands, including the BUI itself. All of the following commands have built-in documentations available with `-h` or `--help` flags:  

#### cxsystem2 

This command (all in lower letters and case sensitive) is the main command of the `CxSystem2` and can be used to run the django server for BUI or run simulations by passing the anatomy and physiology configuration files. 

#### cxconfig 

CxSystem2 supports `csv` and `json` for importing/exporting configuration files. To convert the configuration files, use the `cxconfig` and pass the path to the configuration file path as its argument. This command recognizes the file type and convert it to the alternative extension. 

#### cxcluster 

Use `cxcluster` to download the results from the cluster. `cxcluster` takes in one argument which is the path to the metadata file saved as a result of cluster-run submission. For convenience, at the end of a cluster-run job submission, `CxSystem2` prints the command that should be run to retrieve the result. 

#### cxviz 

TBD

## Citation

If you use CxSystem2 for your work, we kindly ask you to cite any of our related articles: 

```
Andalibi, V., Hokkanen, H., Vanni, S., Controlling complexity of cerebral cortex simulationsâ€”I: CxSystem, a flexible cortical simulation framework, 2019, Neural computation 
```
<br>

```
Hokkanen, H., Andalibi, V., Vanni, S., Controlling complexity of cerebral cortex simulationsâ€”II: Streamlined microcircuits, 2019, Neural computation 
```

## Support

You are encouraged to use <a href="https://github.com/VisualNeuroscience-UH/CxSystem2/issues" target="_blank">Github's Issues</a> to report bugs, or request enhancements or new features.

## Team 

- [Vafa Andalibi](https://www.andalibi.me)
- [Henri Hokkanen](https://github.com/henhok)
- [Simo Vanni](https://scholar.google.fi/citations?user=nRiUf30AAAAJ&hl=en)

## License

[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) 

- **[GPL-3-Clause](https://www.gnu.org/licenses/gpl-3.0.en.html)**
- Copyright 2019 Â© <a href="http://www.helsinki.fi/visualneuroscience/" target="_blank">University of Helsinki</a>.

***
<sub>[1] Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Sanchez, C. A., â€¦ SchÃ¼rmann, F. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell, 163(2), 456â€“492. http://doi.org/10.1016/j.cell.2015.09.029</sub>

<sub>[2]Heikkinen, H., Sharifian, F., VigÃ¡rio, R., & Vanni, S. (2015). Feedback to distal dendrites links fMRI signals to neural receptive fields in a spiking network model of the visual cortex. Journal of Neurophysiology, 114(1), 57â€“69. http://doi.org/10.1152/jn.00169.2015</sub>


