Overview

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QuB is a program designed to make single channel records easier to analyze. With QuB's user-friendly graphical interface, you can

QuB has applications in neurophysiology, electrophysiology, biophysics, etc. It was built to ease analysis of single channel patch clamp records from electrophysiological experiments, but can be used to evaluate any data which is in the form of single, stochastic events.

See also: the selection of Papers about QuB and Research using QuB

Data Formats
QuB can read and write .abf, .pul, .ldt, .dat, .qdf, .txt, .wav, and .dwt files. See Data Theory#Data File Types

Features

  • allows continuous workflow from data acq to final results without switching programs or saving&reopening intermediate files
  • multi-threaded:
    • concurrent processing of multiple files
    • interruptible algorithms
  • multiple open data files:
    • sampled and/or idealized
    • reads (qdf, ldt, dat, abf, pul, wav, ascii, dwt)
    • lo and hi-res displays
    • "selection lists" contain sub-ranges for analysis
      • built by hand or algorithm (see utility functions below)
      • labeled selections allow on-screen annotation
    • baseline correction through linear interpolation
    • low-pass filtering
    • experimental conditions (e.g. Ligand concentration) per file
    • edit data
    • copy, print image of selected data
    • "Data Notes" text-entry area
      • saved with each data file
      • search disk for data with notes containing ...
    • saved with analysis history, including:
      • idealization
      • baseline correction
      • display settings
      • experimental conditions
      • selection lists
      • results of analysis (rate constants, Popen, etc)
      • comments entered in "Data Notes" window
  • overlapping-traces display for selection lists:
    • can display averages or arbitrary functions of selections
  • histograms of selection(s):
    • amplitude
    • duration
    • spectrum
  • multiple open model files:
    • graphically build and edit
    • each rate can be sensitive to concentration of one of several ligands
    • copy or print image
  • classic QUB algorithms:
    • Simulation
    • SKM -- Segmental K-Means idealization
    • MIL -- Maximum interval likelihood rate optimization
    • MPL -- Maximum point likelihood rate optimization
    • Model search -- evaluate all model topologies with MIL
    • Model merge -- combine two models into one aggregate model
  • new algorithms:
    • Idl/Base -- idealize data with uneven baseline using HMM + Kalman
    • MIP -- maximum idealized point likelihood rate optimization
    • Mac -- solve single-channel rate constants from macroscopic data
    • Staircase -- solve rate constants for staircase data e.g. kinesin fluorescence position
    • Exp -- fit macroscopic data with exponentials
    • constructive model search -- build star- or chain-shaped models by adding states until likelihood plateaus
  • utility functions:
    • I-V and dose-response plots
    • stats of idealized data (occupancy probability, mean amps, first latency)
    • build selection lists
      • every N points
      • bursts separated by closure >= Tcrit
      • N points surrounding each rise/fall
  • results browser:
    • shows computed quantities for each data selection
      • as table
      • as scatter plots
      • as histograms
    • allows grouping of heterogeneous selections visually or mathematically into new selection lists
    • shows models, before and after
    • shows histograms with predicted fit curves
  • curve fitting:
    • all histograms, charts, data
    • nonlinear least-squares
    • multiple components
    • built-in or custom curves
  • exports data, graphics, and sound:
    • copy and print pictures of data and model
    • export histograms and graphs as pictures, tables, or Excel spreadsheets
    • create Word reports with all of the above plus numbers from Results
    • save data selections as (qdf, ldt, dat, wav, ascii, dwt)
    • convert data or idealization to WAV sound file with freq = f(amp)
  • Data acquisition and stimulation:
    • supports National Instruments, Data Translation, and any sound card
    • auto-detects hardware
    • multiple channels of continuous input and output
    • oscilloscope
    • manual i/o for reading or writing one value at a time
    • graphical design of stimulation protocols for output or simulation
  • multiple custom layouts:
    • hide unnecessary windows and buttons
    • one-click switch between stored layouts
  • Integrated help and tutorials
  • Python scripting:
    • access data, model, results
    • add items:
      • algorithm buttons
      • built-in curves for fitting
      • external reports
      • stimulus protocol elements
      • wizards
      • burst-selection algorithms
  • qubtree file format:
    • holds arbitrary tree-structured data
    • files are extensible and backward-compatible
      • information added by newer versions is ignorable by older ones
    • library and documentation available [1]
      • supports c++, Python, Delphi
    • used for data (qdf), data-session (qsf), model (qmf), protocol (qpf)


The programs in the QuB Software Suite are copyright The Research Foundation State University of New York. The software is intended for personal use only, and may not be redistributed or sold in any form.


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