Welcome to HJCFIT’s documentation!

HJCFIT provides full maximum likelihood fitting of a kinetic mechanism directly to the entire sequence of open and shut times, with exact missed events correction. The package is derived from the DCPROGS suite and consists of a C++ implementation of the Likelihood calculations along with Python wrappers.

The name of the program is an acronym for Hawkes, Jalali & Colquhoun, whose papers in 1990 and 1992 (HJC92) described the exact solution of the missed event problem, which is the basis of the program. The HJCFIT method was first described by Colquhoun, Hawkes & Srodzinski in 1996 (CHS96).

For a description of the methods involved, see [CH82], [HJC92], [CH95b], [CH95a], [CHS96].

Contents:

• User Guide
  • The \(Q\)-matrix
  • Likelihood \(L(Q)\)
  • Missed-Events transition densities \({}^eG(t)\)
  • Ideal transition densities \(\mathcal{G}(t)\)
  • Equilibrium vectors
  • Exact Survivor Function \(R_A(t)\)
  • Approximate Survivor Function \(R_A(t)\)
  • Determinant Equation \(W(s) = sI - H(s)\)
  • Searching for Roots
  • How to read this manual
• Application Programming Interface:
  • C++ API Reference
  • Python API Reference
• Examples of the use of HJCFIT
  • CB Model
  • CH82 Model
  • CH82 – optimization
  • CHS vector
  • CKF Model
  • Distribution histograms and individual benchmarks
  • HJCFIT- maximum likelihood fit of single-channel data: a simple example
  • HJCFIT- maximum likelihood fit of single-channel data:
  • MissedEvents
  • OpenMP example
  • Time series
  • Approx Survivor
  • Asymptotic vs Exact for classic Matrix
  • Exact Survivor Function
• Running likelihood calculations in parallel
  • OpenMP
  • MPI
• Multi-precision math
• Building and installing HJCFIT:
  • Building and installing HJCFIT
  • Running HJCFIT on Archer
  • Building documentation
  • Customising build and install

Indices and tables

• Index

• Module Index

• Search Page

[CH82]

D. Colquhoun and A. G. Hawkes. On the stochastic properties of bursts of single ion channel openings and of clusters of bursts. Philosophical Transactions of the Royal Society of London. B, Biological Sciences, 300(1098):1–59, December 1982. URL: http://rstb.royalsocietypublishing.org/content/300/1098/1 (visited on 2013-04-18), doi:10.1098/rstb.1982.0156.

[CH95a]

D. Colquhoun and A. G. Hawkes. A q-matrix cookbook. In B Sakmann and E Neher, editors, Single-channel recording, pages 589–633. Plenum Press, New York, 2nd edition, 1995.

[CH95b]

D. Colquhoun and A. G. Hawkes. The principles of the stochastic interpretation of ion channel mechanisms. In B Sakmann and E Neher, editors, Single-channel recording, pages 397–482. Plenum Press, New York, 2nd edition, 1995.

[CHS96]

D. Colquhoun, A. G. Hawkes, and K. Srodzinski. Joint distributions of apparent open and shut times of single-ion channels and maximum likelihood fitting of mechanisms. Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences, 354(1718):2555–2590, November 1996. URL: http://rsta.royalsocietypublishing.org/content/354/1718/2555 (visited on 2013-04-16), doi:10.1098/rsta.1996.0115.

[HJC92]

A. G. Hawkes, A. Jalali, and D. Colquhoun. Asymptotic distributions of apparent open times and shut times in a single channel record allowing for the omission of brief events. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 337(1282):383–404, September 1992. URL: http://rstb.royalsocietypublishing.org/content/337/1282/383 (visited on 2013-04-26), doi:10.1098/rstb.1992.0116.