QUB — Markov simulation and analysis for single molecules and ensembles

Quick start: QUB Online Fitness X-Means Movie Maker

QMJ format encodes a QUB state model in JavaScript Object Notation (JSON). Here's an example:

{
    "channelCount":1,
    "IeqFv":false,
    "balanceLoops":true,
    "vRev":0,
    "states": [
	{"Class":0,"Pr":0,"x":25,"y":50,"Label":"","Index":0},
	{"Class":1,"Pr":0,"x":75,"y":50,"Label":"","Index":1}
    ],
    "classes": [
	{"Amp":0,"Std":0.1,"Cond":0,"CondStd":0.1,"Index":0},
	{"Amp":1,"Std":0.1,"Cond":10,"CondStd":0.1,"Index":1}
    ],
    "rates":[
	{"From":0,"To":1,"k0":10,"k1":0,"k2":0,"Ligand":"","Voltage":"","Pressure":"","Index":0},
	{"From":1,"To":0,"k0":100,"k1":0,"k2":0,"Ligand":"","Voltage":"","Pressure":"","Index":1}
    ],
    "constraints":[
	{"Type":"FixRate","States":[1,0],"Index":0}
    ],
    "modelName":"twostate",
    "modelAbout":"Basic closed-open model, with a constraint fixing the value of k0 closing"
}

Some notes:

• Each state has a class number, shown onscreen as its color (black, red, ...). States in the same class have identical measurements, given in "classes."
• When IeqFv is false, a class's measurements belong to the normal distribution (class.Amp +/- class.Std).
• When IeqFv is true, they belong to the distribution (classes[0].Amp + (V - vRev)*class.Cond +/- (V - vRev)*class.CondStd)
• vRev (the reversal potential) has units mV
• Rates should be given in symmetric pairs, i.e. don't list all rates emanating from state 0, then all rates from state 1, ...
• Constraint types are:
  • "FixRate": hold k0 constant
  • "FixExp": hold k1 constant
  • "FixPress": hold k2 constant
  • "ScaleRate": preserve the ratio between two k0 constants
  • "ScaleExp": preserve the ratio between two k1 constants
  • "ScalePress": preserve the ratio between two k2 constants