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 morphology. ASTRO generates stochastically cell nanoscopic protrusions based on their real-world parameters and enables dynamic interactions between the modelled astrocyte 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 interventions. 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:

    Update BRAINCELL (Windows W10/W11 64-bit installers; choose one):
    BrainCell-2026.03_x86_64_Neuron_9_Setup.exe – bundled with NEURON 9.0.2 and Python 3.11
    BrainCell-2026.03_x86_64_Neuron_8_Setup.exe – bundled with NEURON 8.2.2 and Python 3.11
    No Anaconda or separate NEURON installation is required. Only one of the two versions can be installed at a time.
    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).

    AI Agent Resources: Get started with BRAINCELL using our comprehensive guides:

    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: The graphical environment is not yet available on these platforms. To run an exported model, compile the mechanisms with nrnivmodl (put the MOD files from Mechanisms/Common/MOD_files and Mechanisms/Neuron/MOD_files – or Mechanisms/Astrocyte/MOD_files for astrocyte models – into one folder and run nrnivmodl there; the nrnmech.dll files in the package are Windows-only), then launch via nrniv -python <exported_model>.hoc

Done! BrainCell window opens (Windows only).

Category 2 – Fresh Install

Nothing installed yet

Windows (Easiest Method)

All-in-One Installer (Recommended):

  1. Download BrainCell-2026.03_x86_64_Neuron_9_Setup.exe (NEURON 9.0.2) or BrainCell-2026.03_x86_64_Neuron_8_Setup.exe (NEURON 8.2.2)
  2. Password available after forum registration
  3. Run the installer
  4. Follow installation prompts
  5. Done! Launch BrainCell from Start Menu or Desktop

Time: 15-30 minutes

Manual Installation (Alternative):

  1. Install Anaconda 2023.09 (all versions, SHA256: 810da8bff79c10a708b7af9e8f21e6bb47467261a31741240f27bd807f155cb9)
    • BrainCell is tested with Anaconda3 2023.09-0 (Python 3.11.5). Download it from the official Anaconda archive; do not use third-party mirrors.
    • 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 the Xcode Command Line Tools (needed by nrnivmodl to compile mechanisms): xcode-select --install
  2. Install Anaconda 2023.09 (Python 3.11): Anaconda3-2023.09-0-MacOSX-arm64.pkg for Apple Silicon or Anaconda3-2023.09-0-MacOSX-x86_64.pkg for Intel Macs. Newer Anaconda releases ship a Python that NEURON 8.2.2 does not support.

  3. Install NEURON and the Python packages into Anaconda:

    pip install neuron==8.2.2
pip install -r https://neuroalgebra.net/assets/requirements.txt
  4. 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

# Compiler for nrnivmodl (Ubuntu/Debian)
sudo apt-get install build-essential

# Install NEURON and Python packages into Anaconda
pip install neuron==8.2.2
pip install -r https://neuroalgebra.net/assets/requirements.txt

# 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  # /Applications/NEURON only if installed from the .pkg

Restart Mac

Linux:

rm -rf ~/anaconda3 ~/.conda  # removes Anaconda together with pip-installed NEURON

Restart

Now Follow Category 2

After removing everything, follow Category 2 Fresh Install.

Recommended: Use the all-in-one installer for Windows: BrainCell-2026.03_x86_64_Neuron_9_Setup.exe (NEURON 9.0.2) or BrainCell-2026.03_x86_64_Neuron_8_Setup.exe (NEURON 8.2.2).

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) — graphical environment, full functionality
  • macOS / Linux — running exported models only (GUI support in development)

BrainCell Version: 2026.03
Installation Guide Last Updated: March 2026