Welcome to HJCFIT’s documentation!¶
The goal of HJCFIT is to provide a collection of tools for scientific research on ion channels. The package is derived from the DCPROGS suite and consists of a C++ implementation of the Likelihood calculations along with Python wrappers. The code is a port of Fortran code with ~30 years usage at University College London. The rationale is to preserve and cultivate these tools for future research applications.
For a description of the methods involved, see [CH82], [HJC92], [CH95b], [CH95a], [CHS96].
Contents:
- User Guide
- Application Programming Interface:
- 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
- Multi-precision math
- Building and installing HJCFIT:
Indices and tables¶
| [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, 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, 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, doi:10.1098/rstb.1992.0116. |