Namdinator

Namdinator: Cryo-EM Data Processing Pipeline

Project Overview

Namdinator is a specialized scientific tool developed for Aarhus University's Department of Molecular Biology and Genetics. It helps researchers process cryo-electron microscopy (cryo-EM) data, automating a formerly complex and time-consuming analytical process.

The Challenge

The research team at Aarhus University faced several challenges with their cryo-EM data processing:

• Manual processing was extremely time-consuming
• Results could vary depending on the researcher's approach
• Limited computational resources on local workstations
• Need for a collaborative platform accessible to the entire research team
• Complex model refinement requiring specialized computational methods

Our Solution

We developed a comprehensive web-based pipeline that:

1. Accepts Raw Data Input: Researchers can upload their cryo-EM map and initial model coordinates
2. Processes Data Through Multiple Stages: The system executes a series of computational steps including NAMD simulation and real-space refinement
3. Provides Interactive Results: Researchers can visualize and analyze the refined models through a user-friendly interface
4. Manages Computational Resources: Tasks are scheduled and distributed across high-performance computing resources

Technical Implementation

The project was implemented as a multi-tier system:

• Frontend: Built with modern web technologies including HTML5, CSS, and JavaScript
• 3D Visualization: Advanced JavaScript libraries for interactive 3D visualization of molecular structures
• Backend: PHP-based server infrastructure handling data processing and job management
• High-Performance Computing: Integration with HPC clusters for intensive computational tasks
• Database: Efficient storage and retrieval of molecular data and processing results

The backend services were deployed on a high-performance computing cluster, with a web frontend providing easy access to researchers worldwide.

Results

The Namdinator pipeline has transformed cryo-EM data processing at Aarhus University:

• Efficiency: What once took days now completes in hours
• Accessibility: Researchers can submit jobs from anywhere with internet access
• Standardization: Consistent processing methodology ensures comparable results
• Scientific Impact: The tool has been cited in numerous peer-reviewed publications
• Global Reach: The tool is now used by researchers at multiple institutions internationally, including leading research centers and universities worldwide