Computational Tools


OPEN SOURCE COMMITMENT: Our software packages are open for you to download, install, and explore under the permissive 3-clause BSD license.


  1. ASTRO is a computational platform for constructing and exploring realistic multi-compartmental astrocyte models that can be biophysically interrogated in NEURON computational environment, on the scale from nanometers to the entire cell moprhology. ASTRO generates stochastically cell nanoscopic protrusions based on their real-world parameters and enables dynamic interactions between the modelled astorcyte and the surrounding 3D tissue environment.

    Documentation: PDF file.

  2. ARACHNE is designed to model multi-cell spiking networks of neurons and astrocytes. In ARACHNE environment, the network organisation, optimisation, and execution benefit from pre-set, optimised parallel algorithms for remote computations and a friendly user interface operated from your own computer. A neuroscientist without IT background should be able to incorporate the representative variety of biophysical mechanisms pertinent to nerve and astroglial cells, within a single network model.

    Documentation: PDF file.

  3. BRAINCELL is a platform that combines theoretical aspects of computational neuroscience with real-world aspects of cell and tissue physiology of the brain, including the capacity to replicate some common experimental designs. The immersive modelling environment enables neuroscientists and neurologists to investigate brain cellular mechanisms and assess the physiological effects of experimental or therapeutic interventionse. Its key features include stochastic generation of nano-morphology and function, stop-save-go control of simulation runs, dynamic extracellular and inter-cellular interactions, adaptive import of cell morphologies.

    Installation: BrainCell-2025.03_x86_64_Setup.exe (Windows W10/W11 64-bit installer)
    Important note: To run the Setup you will require password which you can find after [Registration at our FORUM].

    Installation instructions:

    Documentation: PDF file, or in Word format BRAINCELL_User_Guide.docx (alternatively, check experimental PDF->HTML conversion).

    Additional Resources:


  4. CLOUD COMPUTATION PLUGIN: we are currently working with Neuroscience Gateway - a portal for computational Neuroscience to enable computations on their HPC supercomputer. When the integration is complete, registered Neuroalgebra users will be able to benefit from the HPC power and run our tools on a supercomputer cluster in the cloud.

    Installation: Please inquire about the current status of our cloud computation package in a discussion group on our forum. To register at the forum follow this link: [Registration at our FORUM].


BrainCell Installation Guide

Choose Your Category

Category 1: NEURON + Python already working → Quick Setup
Category 2: Clean system (nothing installed) → Fresh Install
Category 3: Partial installation or problems → Clean Reinstall

Category 1 – Quick Setup

You already have NEURON and Python working

  1. Download cloudpackage-v1.zip from forum - Registration required
  2. Create folder: C:\braincell (Windows) or ~/braincell (Mac/Linux)
  3. Unblock the ZIP: Right-click → Properties → ☑️ Unblock → Apply (Windows only)
  4. Extract ZIP to your folder
  5. Windows: Unblock init.bat, then double-click it
  6. Mac/Linux: Run chmod +x init.sh && ./init.sh

Done! BrainCell window opens.

Category 2 – Fresh Install

Nothing installed yet

Windows (Easiest Method)

All-in-One Installer (Recommended):

  1. Download BrainCell-2025.03_x86_64_Setup.exe
  2. Password available after forum registration
  3. Run the installer
  4. Follow installation prompts
  5. Done! Launch BrainCell from Start Menu or Desktop

Includes: Anaconda + NEURON + BrainCell
Time: 15-30 minutes

Manual Installation (Alternative):

  1. Install Anaconda 2023.09
    • Choose “Just Me”
    • ☑️ Add Anaconda to PATH
    • Restart Windows
  2. Install NEURON 8.2.2
    • Use default options
    • Restart Windows
  3. Follow Category 1 steps

Time: 30-60 minutes

macOS

  1. Install Anaconda
  2. Install NEURON
  3. Follow Category 1 steps

Time: 30-60 minutes

Linux

# Install Anaconda
wget https://repo.anaconda.com/archive/Anaconda3-2023.09-0-Linux-x86_64.sh
bash Anaconda3-2023.09-0-Linux-x86_64.sh
source ~/.bashrc

# Install NEURON
sudo apt-get install neuron  # Ubuntu/Debian

# Follow Category 1 steps

Time: 30-60 minutes

Category 3 – Clean Reinstall

Partial installation or not working

⚠️ Critical: Remove Everything First

Windows:

  1. Uninstall NEURON and Anaconda (Settings → Apps)
  2. Delete folders: C:\nrn, C:\Users\[You]\anaconda3
  3. Restart Windows

macOS:

rm -rf ~/anaconda3 ~/.conda /Applications/NEURON ~/neuron

Restart Mac

Linux:

rm -rf ~/anaconda3 ~/.conda ~/neuron
sudo apt-get remove --purge neuron  # if installed via apt

Restart

Now Follow Category 2

After removing everything, follow Category 2 Fresh Install.

Recommended: Use the all-in-one installer BrainCell-2025.03_x86_64_Setup.exe for Windows.

Time: 45-75 minutes

Testing in Windows Sandbox (Reviewers & Advanced Users)

For those with Windows 10/11 Pro, you can test BrainCell in an isolated environment without affecting your main system:

  1. Enable Windows Sandbox:
    • Press Win + R
    • Type: optionalfeatures
    • Check ☑️ Windows Sandbox
    • Click OK and restart
  2. Follow detailed sandbox testing guide: Windows Sandbox Setup Guide - Registration required

Benefits:

  • Clean testing environment
  • No impact on main system
  • Easy repeatability
  • Complete reset between sessions

Support & Resources

System Requirements

Minimum:

  • RAM: 4 GB (8 GB recommended)
  • Disk Space: 5 GB free
  • Processor: 64-bit

Operating Systems:

  • Windows 10/11 (64-bit)
  • macOS 10.15+ (Catalina or later)
  • Linux: Ubuntu 20.04+, Debian, Fedora

BrainCell Version: 2025.03
Installation Guide Last Updated: January 2026