GEMMER

GEMMER integrates and visualizes multi-scale interaction data for Saccharomyces cerevisiae to support analysis of physical, regulatory, and genetic networks.

Key Features:

• Interaction visualization: Generates visual representations of physical, regulatory, and genetic interactions among genes and proteins.
• Data integration: Combines datasets from multiple existing databases into unified network representations.
• Functional annotations: Incorporates functional attributes associated with genes and proteins.
• Temporal expression: Includes temporal expression pattern data for dynamic analysis.
• Localization and abundance: Integrates cellular localization and abundance level information for network nodes.
• Multi-scale modeling support: Extracts and represents data relevant for multi-scale modeling of biological systems.
• Data and image export: Provides export of visualizations as images and of underlying network data.
• Technical stack: Employs Python for backend processing, the JavaScript library D3.js for dynamic visualization, PHP for server-side scripting, and JSON for data interchange.

Scientific Applications:

• Network analysis: Analysis of protein–protein, protein–DNA, and genetic interaction networks in Saccharomyces cerevisiae.
• Systems biology: Integration of multi-dimensional data for systems-level studies and hypothesis generation.
• Temporal dynamics: Examination of temporal expression patterns within interaction networks.
• Spatially informed modeling: Use of cellular localization and abundance data to inform spatial and quantitative models.
• Multi-scale modeling: Support for extracting representations and parameters useful in multi-scale computational models.

Methodology:

Backend processing in Python; server-side scripting in PHP; dynamic visualization with the JavaScript library D3.js; data interchange using JSON; integration and extraction of datasets from existing databases.