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Installation Guide

In order to run the application on your system, it is essential to have these prerequisites installed on your computer. Please follow the steps below to set up the dependencies based on your current operating system.

Video Tutorial

A step-by-step video tutorial for the installation procedure is available on our YouTube channel: BNSB Lab - IITH

NodeJS Installation

Step 1: Download Node.js

Go to the official Node.js download page and download the installer for your operating system: https://nodejs.org/

  • Windows Windows NodeJS Installation

  • MacOS MacOS NodeJS Installation

  • Linux Linux NodeJS Installation

Step 2: Install Node.js

Run the downloaded installer and follow the on-screen instructions:

  • Accept the license agreement
  • Choose the installation directory (default is recommended)
  • Ensure “Add to PATH” is checked
  • Complete the installation

Step 3: Verify Installation

Open a terminal or command prompt and run:

node --version

npm --version

If both commands return version numbers, Node.js and npm have been installed successfully.

Python Installation (Python 3.12)

Step 1: Download Python

Go to the official Python website and download Python 3.12 for your operating system:

https://www.python.org/downloads/

  • Windows Download the Windows installer (64-bit).

  • MacOS Download the macOS universal installer.

  • Linux Use your system package manager or build from source (recommended for Python 3.12).

Step 2: Install Python

Windows

  • Run the downloaded .exe file
  • Check “Add Python to PATH” (very important)
  • Click Install Now
  • Complete the installation

MacOS

  • Open the downloaded .pkg file
  • Follow the installation wizard
  • Python will be installed under /usr/local/bin/python3

Linux (Ubuntu / Debian example)

sudo apt update
sudo apt install python3.12 python3.12-venv python3.12-dev

If Python 3.12 is not available via apt, install it from source:

sudo apt install build-essential libssl-dev zlib1g-dev \
libncurses5-dev libncursesw5-dev libreadline-dev libsqlite3-dev \
libgdbm-dev libbz2-dev liblzma-dev tk-dev wget

wget https://www.python.org/ftp/python/3.12.0/Python-3.12.0.tgz
tar -xf Python-3.12.0.tgz
cd Python-3.12.0
./configure --enable-optimizations
make -j$(nproc)
sudo make altinstall

Step 3: Verify Installation

Open a terminal or command prompt and run:

python --version

or

python3 --version

You should see output similar to:

Python 3.12.x

Step 4: Verify pip (Python Package Manager)

pip --version

or

pip3 --version

Download and Run NAViFluX

Step 1: Get the Source Code

You can obtain the software in either of the following ways:

  • Option 1: Clone the repository
git clone "https://github.com/bnsb-lab-iith/NAViFluX"
  • Option 2: Download the repository as a ZIP file and extract it

Step 2: Install Dependencies and Run

Follow the instructions based on your operating system:

  • Windows
.\install.ps1
.\run.ps1
  • Linux
./install.sh
./run.sh
  • MacOS
./install.sh
./run_mac.sh

If the Scripts Don’t Work (Manual Setup)

No worries — you can still run the application manually by following the steps below.

Step 1: Start the Frontend

1. Open a terminal and navigate to the client folder:

cd client

2. Install the required Node.js dependencies:

npm install

3. Start the development server:

npm run dev
4. Open the link on your browser

Step 2: Start the Backend

1. Open a new terminal window and navigate to the backend directory.

2. Create a Python virtual environment:

python -m venv .venv

3. Activate the virtual environment based on your OS:

  • Windows
.venv\Scripts\activate
  • MacOS / Linux
source .venv/bin/activate

4. Install Python dependencies:

pip install -r requirements.txt

5. Run the Flask server:

flask run

Performance Benchmarks

The typical runtimes for three analyses implemented in NAViFluX are provided below. NAViFluX was tested on different machines with variable CPU, RAM, and OS configurations.

Two GSMNs of different metabolite–reaction dimensions were used to evaluate the runtime performance:

  • iJO1366 — 2583 Reactions, 1805 Metabolites
  • RECON1 — 3741 Reactions, 2766 Metabolites

64 GB RAM, Intel i9 Processor, 32-Core CPU (Linux)

Model Flux Variability Analysis Single Rxn Deletion Flux Sampling
iJO1366 3.0196 1.7292 35.2431
RECON1 7.7967 3.5099 77.6662

16 GB RAM, Apple M4, 10-Core CPU (macOS)

Model Flux Variability Analysis Single Rxn Deletion Flux Sampling
iJO1366 20.691 11.6096 49.5542
RECON1 36.216 13.5691 106.8398

16 GB RAM, Intel i7 Processor, 4-Core CPU (Windows)

Model Flux Variability Analysis Single Rxn Deletion Flux Sampling
iJO1366 74.6648 40.4138 96.3714
RECON1 113.658 56.7247 781.1803

Note

All values indicate NAViFluX analysis runtime in CPU seconds.