Getting Started with BioSpring

Quick Start Guide

BioSpring offers multiple ways to get started with interactive molecular simulations of elastic network models:

Option 1: MolPlay Interactive Platform

For an interactive, user-friendly experience, we recommend using MolPlay, it comes with BioSpring built in.

MolPlay provides a comprehensive graphical interface for exploring molecular simulations. For detailed installation instructions, please refer to the dedicated MolPlay Getting Started Guide.

Key steps include:

  • Download the MolPlay ISO image
  • Create a bootable USB drive using Rufus or Etcher
  • Boot from the USB drive and explore BioSpring simulations (among others)

Option 2: Docker Container

For users preferring a containerized environment, BioSpring offers a Docker image:

Prerequisites

  • Docker installed on your system
  • Minimum Docker version: 20.10

Quick Installation

# Pull the latest BioSpring Docker image
docker pull ghcr.io/lbt-cnrs/biospring:latest

# Go to some example directory, for instance from git
# where *.nc and *.msp input files are available
cd example/2particles

# Run the BioSpring container non-interactively
docker run --init -v ./:/data ghcr.io/lbt-cnrs/biospring \
       biospring -s /data/model.nc -c /data/param.msp

The above merely runs a (non-interactive) BioSpring simulation for testing. You do have the option to run the container so that it exposes a network port for the IMD protocol, then you can connect UnitMol or VMD to that port.

  • Additional Docker Options

    • IMD port exposure: Use -p and --port to enable connections 

      # Run the BioSpring container exposing network port 3000
docker run -p 3000:3000 --init -v ./:/data ghcr.io/lbt-cnrs/biospring \
      biospring -s /data/model.nc -c /data/param.msp --wait --port 3000

Option 3: Installation from Source

For advanced users and developers, detailed source installation instructions are available in our Source Installation Guide.

Next Steps

After installation, we recommend:

  1. Exploring example molecular systems
  2. Reviewing tutorial documentation
  3. Experiment with your own favorite systems.. and let us know about it!

Exploring BioSpring Examples

Tips for Beginners

  • Start with simpler examples like “the guanylate kinase enzyme” before moving to more complex systems
  • Take time to read the documentation for each example before launching
  • Experiment with different interactions and observe how the system responds
  • Don’t hesitate to restart a simulation if you want to try a different approach

A description for the examples is provided here.

Exploring More Examples

As you become comfortable with basic simulations, explore more complex examples. A broader selection will be added to the github page and to MolPlay soon.

Challenge yourself with different molecular systems and interaction scenarios!

Accessing Help and Documentation

If you need additional assistance:

  1. Ask our (experimental) Chatbot
  2. Look for video tutorials that may be available for specific examples
  3. Check our Frequently Asked Questions (F.A.Q.) section
  4. Use GitHub’s issues tracking
  5. Note that BioSpring integrates unit & regressions tests, you may check those for validation of your installation!

If you do get stuck, do not panic! You can always drop us an email.

Remember, practice and experimentation are key to mastering BioSpring.. and there may be bugs, of course!

Explore BioSpring examples