NETrex is a real-time neural network modeling and dynamic clamp application for neuroscience research. It combines the functionality of the legacy NetSim (simulation) and NetClamp (dynamic clamp) applications into a single unified program.

Key features:

• Build networks of model neurons with Hodgkin-Huxley conductances, synapses, gap junctions, and current injection electrodes
• Run pure simulations or real-time dynamic clamp experiments with NI-DAQmx hardware
• Real-time trace plotting, CSV data export, and configurable timing protocols
• Cross-platform: works on Windows, Linux, and macOS

Author: E. Brady Trexler, Ph.D.
License: GNU General Public License v3
Website: hudsonvalleysci.com

Pre-built binaries are available on the Releases page.

1. Download NETrex-Windows-x64.zip from the latest release
2. Extract the zip to a folder (e.g., C:\NETrex)
3. Double-click NETrex.exe to run
4. For dynamic clamp with NI hardware: Install the free NI-DAQmx Runtime from ni.com. NETrex will automatically detect your DAQ device.
5. For simulation only: No additional software needed — just run the app

1. Download NETrex-macOS.zip from the latest release
2. Extract the zip — you'll get NETrex.app
3. Drag NETrex.app to your Applications folder
4. Before first launch, open Terminal and run:

   xattr -cr /Applications/NETrex.app

   This removes the macOS quarantine flag that blocks unsigned apps downloaded from the internet.
5. Double-click NETrex.app to run
6. Note: macOS runs in simulation mode only (no NI-DAQmx hardware support). A mock DAQ backend is included for testing dynamic clamp networks.

1. Download NETrex-Linux-x64.zip from the latest release
2. Extract and make executable: chmod +x NETrex
3. Run: ./NETrex
4. Requires Qt 5 libraries (sudo apt install libqt5widgets5 on Ubuntu/Debian)
5. For dynamic clamp: Install the NI-DAQmx driver for Linux

git clone <repo-url> NETrex
cd NETrex
mkdir build && cd build
cmake ..
make NETrex
./NETrex

All other dependencies (nlohmann/json, NI-DAQmx headers) are included in the repository.

This is the primary target for dynamic clamp experiments.

1. Install prerequisites:

   • Visual Studio 2019 or 2022 (Community edition is free) — select "Desktop development with C++"
   • CMake (3.15 or newer)
   • Qt 5.15 — install the MSVC 2019 64-bit component
   • NI-DAQmx driver — install the full driver (not just Runtime)

2. Set up environment:

   set CMAKE_PREFIX_PATH=C:\Qt\5.15.2\msvc2019_64

   Adjust the path to match your Qt installation.

3. Build:

   git clone <repo-url> NETrex
   cd NETrex
   mkdir build && cd build
   cmake .. -G "Visual Studio 17 2022" -A x64
   cmake --build . --config Release --target NETrex

4. Run:

   Release\NETrex.exe

   CMake will automatically detect the NI-DAQmx library and enable hardware support. You should see this during cmake configuration:

   -- NI-DAQmx found: C:/.../nidaqmx.lib
   

5. Deploy (create standalone folder):

   mkdir deploy
   copy Release\NETrex.exe deploy\
   cd deploy
   windeployqt NETrex.exe

   The deploy folder can be zipped and shared — it contains all needed Qt DLLs.

NI-DAQmx is supported on select Linux distributions (RHEL, CentOS, Ubuntu, openSUSE).

1. Install prerequisites:

   # Ubuntu/Debian
   sudo apt install build-essential cmake qt5-default
   
   # Fedora/RHEL
   sudo dnf install gcc-c++ cmake qt5-qtbase-devel

2. Install NI-DAQmx (optional, for hardware): Download the Linux driver from ni.com. Follow NI's installation instructions. The library installs to /usr/lib/x86_64-linux-gnu/libnidaqmx.so.

3. Build:

   git clone <repo-url> NETrex
   cd NETrex
   mkdir build && cd build
   cmake ..
   make NETrex

   If NI-DAQmx is installed, cmake will report:

   -- NI-DAQmx found: /usr/lib/x86_64-linux-gnu/libnidaqmx.so
   

   If not installed, it will use the mock backend for testing.

4. Run:

   ./NETrex

NI-DAQmx is not available on macOS. NETrex runs with a mock DAQ backend that simulates a biological cell with Hodgkin-Huxley currents, allowing full development and testing of networks.

1. Install prerequisites:

   # Install Xcode command line tools
   xcode-select --install
   
   # Install Homebrew packages
   brew install cmake qt@5

2. Build:

   git clone <repo-url> NETrex
   cd NETrex
   mkdir build && cd build
   cmake .. -DCMAKE_PREFIX_PATH=$(brew --prefix qt@5)
   make NETrex

3. Run:

   ./NETrex

When a network contains only model cells (no biological cells), NETrex runs as a pure simulator. The network is updated at the requested sample rate using RK4 integration, and results are plotted in real time.

When a network contains one or more biological cells, NETrex automatically switches to dynamic clamp mode:

1. Analog input channels read membrane voltages from the amplifier
2. The network model computes synaptic/intrinsic currents based on the measured voltages
3. Computed currents are written to analog output channels and injected into the cell

The timing protocol supports three phases:

• Before: DAQ is reading but no current is injected (baseline)
• During: Active dynamic clamp — currents are computed and injected
• After: DAQ is reading but current injection stops (recovery)

• Model Cell — Integrate-and-fire neuron with configurable currents
• Vm Playback Cell — Plays back a voltage waveform from a file
• Biological Cell — Represents a real neuron connected via DAQ hardware

• Hodgkin-Huxley conductance (HH, HH2)
• Gap junction
• Voltage clamp PID
• Generic bidirectional synapse
• Playback current waveform

Networks are saved as JSON files (.json). Example:

{
  "cells": [
    {
      "name": "Cell 1",
      "type": "Model Cell",
      "active": true,
      "currents": [...]
    }
  ],
  "electrodes": [...],
  "synapses": [...]
}

cmake can't find Qt5: Set CMAKE_PREFIX_PATH to your Qt installation:

cmake .. -DCMAKE_PREFIX_PATH=/path/to/qt5

NI-DAQmx not detected: Ensure the full NI-DAQmx driver is installed (not just Runtime). Check that libnidaqmx is in your library path. cmake will print a status message indicating whether the library was found.

Mock backend on Windows/Linux: If you want to develop without hardware, NETrex works fine — it just uses the mock backend. No configuration needed.

cmake --build . --config Release --target NETrex
mkdir deploy
copy Release\NETrex.exe deploy\
cd deploy
windeployqt NETrex.exe

Zip the deploy folder. Recipients need the NI-DAQmx Runtime (free download from ni.com) if using hardware.

# Build with static Qt or use linuxdeployqt:
# https://github.com/probonopd/linuxdeployqt
make NETrex
linuxdeployqt NETrex -appimage

Produces a portable AppImage. Recipients need NI-DAQmx driver for hardware.

make NETrex
macdeployqt NETrex.app -dmg

Produces a .dmg for distribution (simulation only, no DAQ hardware support).