Apps: QUB Express QuB Classic QUBIO Fitness X-Means
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QUB Express

Features in QUB Express and Classic:
  • interactive hidden Markov model building and simulation: simulates recordings from one molecule or an ensemble, at equilibrium or responding to a stimulus protocol
  • baseline correction and event detection: Viterbi and Kalman methods can pick a single-molecule signal out of substantial noise
  • maximum likelihood optimization of model parameters, for single molecule and ensemble data, with constraints
  • burst detection, statistics and clustering: lists "bursts" (event clusters separated by long inactivity), plots properties such as Popen, and algorithmically splits the list into groups (K-Means)
  • measurement and histograms
  • nonlinear least-squares curve fitting of any figure, to any user-entered curve function
  • model search: evaluates likelihood of all connection schemes
  • model merge: combines two models into one, with appropriate constraints
Unique to QUB Express:
  • "live" simulation responds to each change in the model, unless paused
  • streamlined stimulus assignment when optimizing with data that has a stimulus signal
  • the single-molecule optimizer (MIL/MSL) can handle data with a stimulus signal e.g. varying ligand concentration or voltage
  • unlimited undo/redo in the model
  • automatic lab notebook saved as an HTML document while you work; output can be customized, scripted, and/or redirected to other programs
  • fewer clicks, fewer legacy options
  • scriptable, hosts plugins: can record actions as a Python script; some panels are already plugins; 3rd-party plugins welcome
  • runs on Linux, Mac OS X and Windows
Reasons to use QuB Classic instead:
  • data acquisition (or use QUBIO)
  • dynamic clamp: use this custom QuB
  • staircase algorithms: for unidirectional data e.g. molecular motor position
  • Kalman background subtraction: tracks and removes periodic noise
  • misc. options including multi-file extraction, some dose-response simulations, some figures
[QUB Express screenshot]
[QUB Express screenshot 2]

QuB Classic

Features in QUB Classic and Express:
  • interactive hidden Markov model building and simulation: simulates recordings from one molecule or an ensemble, at equilibrium or responding to a stimulus protocol
  • baseline correction and event detection: Markov and Kalman methods can pick a single-molecule signal out of substantial noise
  • maximum likelihood optimization of model parameters, for single molecule and ensemble data, with constraints
  • burst detection, statistics and clustering: lists "bursts" (event clusters separated by long inactivity), plots properties such as Popen, and algorithmically splits the list into groups (K-Means)
  • measurement and histograms
  • nonlinear least-squares curve fitting of any figure, to any user-entered curve function
  • model search: evaluates likelihood of all connection schemes
  • model merge: combines two models into one, with appropriate constraints
Unique to QuB Classic:
  • data acquisition (or use QUBIO)
  • dynamic clamp: use this custom QuB
  • staircase algorithms: for unidirectional data e.g. molecular motor position
  • Kalman background subtraction: tracks and removes periodic noise
  • misc. options including multi-file extraction, some dose-response simulations, some figures
Reasons to use QUB Express instead:
  • "live" simulation responds to each change in the model, unless paused
  • streamlined stimulus assignment when optimizing with data that has a stimulus signal
  • the single-molecule optimizer (MIL/MSL) can handle data with a stimulus signal e.g. varying ligand concentration or voltage
  • unlimited undo/redo in the model
  • automatic lab notebook saved as an HTML document while you work; output can be customized, scripted, and/or redirected to other programs
  • fewer clicks, fewer legacy options
  • scriptable, hosts plugins: can record actions as a Python script; some panels are already plugins; 3rd-party plugins welcome
  • runs on Linux, Mac OS X and Windows
[QuB Screenshot]

QUBIO

  • records and generates analog and digital signals using National Instruments M-series hardware.
[QUBIO Screenshot]

Fitness

  • nonlinear least-squares curve fitting
  • user-defined curves can be any function(series1, series2, ...), with access to functions from numpy and scipy
  • fitting curve can be a user-defined first-order ODE system
  • user-defined weighting can be any column or function of columns
  • strategy script helps automate difficult fits by specifying when to fit parameters and when to hold them
  • resample by delta replaces flat regions of data with a single point, to emphasize dynamic features
  • K-Means clustering divides datapoints into K groups, minimizing square distance from group centroid
  • "X-Means" provides distance- and likelihood-based metrics to help decide which K is best
  • automatic lab notebook saved as an HTML document while you work; output can be customized, scripted, and/or redirected to other programs
  • scriptable, hosts plugins: can record actions as a Python script; some panels are already plugins; 3rd-party plugins welcome
  • runs on Linux, Mac OS X and Windows
Fitness Screenshot]
Fitness Screenshot 2]

X-Means

  • K-Means clustering divides datapoints into K groups, minimizing square distance from group centroid
  • "X-Means" provides distance- and likelihood-based metrics to help decide which K is best
  • clusters based on one or more columns of tabular data
  • runs as a web app in modern web browsers
Go to the X-Means web app
[X-Means Screenshot]