MOSAIC: A Modular Single-Molecule Analysis Interface

MOSAIC is a single molecule analysis toolbox that automatically decodes multi-state nanopore data. By modeling the nanopore system with an equivalent circuit, MOSAIC leverages the transient response of a molecule entering the channel to quantify pore-molecule interactions. In contrast to existing techniques such as ionic current thresholding [Pedone:2009ds][Robertson:2010gm] or Viterbi decoding [Viterbi:1967hq], this technique allows the estimation of short-lived transient events that are otherwise not analyzed.

Nanometer-scale pores have demonstrated potential use in biotechnology applications, including DNA sequencing [Kasianowicz:1996us], single-molecule force spectroscopy [VanDorp:2009tg], and single-molecule mass spectrometry [Robertson:2007jo]. The data modeling and analysis methods implemented in MOSAIC allow for considerable improvements in the quantification of molecular interactions with the channel in each of these applications.

• 1. Introduction
• 2. Data Processing Algorithms in MOSAIC
  • 2.1. ADEPT 2-State
  • 2.2. ADEPT
  • 2.3. CUSUM+
• 3. Getting Started
  • 3.1. Binary Installation
  • 3.2. Source Installation
  • 3.3. Docker Installation
• 4. MOSAIC GUI
  • 4.1. Interface Overview
  • 4.2. Panels A & B: Analysis Setup and Trajectory Viewer
  • 4.3. Panels C,D, & E: Blockade Depth Histogram, Statistics, and Event Viewer
• 5. MOSAIC WEB
  • 5.1. Interface Overview
  • 5.2. Data Source Path
  • 5.3. Analysis Settings
  • 5.4. Analysis Results
• 6. Settings File
  • 6.1. Settings Layout
  • 6.2. Trajectory Settings
  • 6.3. Optimizing Settings
  • 6.4. Default Settings
• 7. Database Structure and Query Syntax
  • 7.1. Metadata Table
  • 7.2. Analysis Settings Table
  • 7.3. Work with SQLite
  • 7.4. Export to CSV
• 8. Scripting and Advanced Features
  • 8.1. Import Data and Run an Analysis
  • 8.2. Advanced Scripting
• 9. Extend MOSAIC
  • 9.1. Read Arbitrary Binary Data Files
  • 9.2. Define Top-Level Functionality
• 10. Publication Quality Figures
  • 10.1. Timeseries Plots
  • 10.2. Histogram Plots
  • 10.3. Contour Plots
• 11. Advanced Analysis
  • 11.1. Capture Rate
• 12. Addons
  • 12.1. Mathematica
  • 12.2. Matlab
  • 12.3. IGOR
• 13. Developer Tools
  • 13.1. Debug Logs
  • 13.2. Function Timing and Profiling
• 14. API Documentation
  • 14.1. MOSAIC Modules
• 15. Bibliography