DC FORTRAN compiled DOS programs
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gino
lf90
AUTPLOT.ICO
CONSAM2.513
CVFIT.ICO
DCPROGS.INI
EKDEMO.INI
EKDIST.ICO
GINO.CON
HJC3X3T.INI
HJCDEMO.PLQ
HJCFIT.EXE
HJCFIT.ICO
HJCFITf.EXE
HJCdemo.PRT
HjcCubeT.ini
Mac_instructions_DCProgs.pdf
PRIMES.DAT
RAUTPLOT.BAT
RCVFIT.BAT
README.md
REKDIST.BAT
RENUM.DAT
RHJCFIT.BAT
RSCAN.BAT
SCALCS.ICO
SCAN.ICO
SCAN.INI
SCANDEM1.BAT
SCANDEMO.BAT
SCBST.EXE
SCBST.ICO
SCBST.INI
SCCOR.EXE
SCJUMP.EXE
SCJUMP.ICO
SCJUMP.INI
SCSIM.EXE
SIMAN.EXE
Scb3x3.ini
Scsim.ini
Scsimdem.ini
VHIST.INI
VPLOT.INI
ad5.exe
adcdma.cmd
adcdma.gxc
autplot.exe
biophysJ.mec
cjfit.ico
cjump5.ico
consam.ico
consmjc2.ssd
cvfit.exe
dcmanuals.pdf
ekdist.exe
ekdist.ini
filtsamp.exe
hjcCubeC.ini
hjcdemo.doc
hjcdemo.ini
hjcfit.ini
plotsamp.exe
qmechdem.mec
qmechs.mec
random.dat
rcjfit.bat
rcjump.bat
rscalcs.bat
rscbst.bat
rsccor.bat
rscdir.bat
rscjump.bat
rscsim.bat
scalcs.exe
scalcs.ini
scan.exe
scansim.scn
scantemp.513
scantemp.ach
scantemp.dat
sccor.ico
sccor.ini
scdir.ico
scsim.ico
scsimdem.prt

README.md

DCDOS

DCDOS repository contains the original compiled DC DOS programs written in Fortran, with GINO graphics.

Some programs have been rewriten in FORTRAN to compile for Windows (HJCFIT and AUTPLOT: see DCWIN repository) and some are being rewriten in pure Python (theoretical calculation programs: see SCALCS repository; curve fitting program: see CVFIT repository) or Python/C++ (see HJCFIT repository). However, some programs are available only for DOS, especially the crucial SCAN program for idealisation of raw single-channel data.

The DOS programs run on most PCs, but to run them on a Windows 7 or Windows 8 machine, you must install DOSBOX first. The following method works on a 64 bit Windows 7 machine (theoretically should work on MAC and Linux machines):

  • Download the programs and stuff needed to run them as a zip file by clicking button'Download ZIP' or by cloning all the repository using git (command 'git clone https://github.com/DCPROGS/DCDOS.git').
  • Download and install DOSBOX from http://www.dosbox.com/
  • Run DOSBOX (eg by clicking the desktop icon)
  • At the Z:> prompt in the DOS box, type mount c c:\DCDOS
  • To go to the virtual disk C which is now the DCDOS folder- type C:\
  • At the C:> prompt you can type HELP for a list of commands, eg type DIR to see the contents of the \dcprogs folder.
  • Type scan to run scan.exe or the name of any other .exe file in the DCDOS folder. A new window appears in which the program runs. You can make it run whole screen by hitting alt-enter (repeat to exit full screen mode). Remember that DOS file names are restricted to 8 characters + 3 character suffix. You can use only letters and numbers in the file name, no spaces or punctuation.
  • When you leave the program you get back to the C:> prompt. Type EXIT to end the DOS emulation.

The instructions for installation and running DC DOS programs on MAC (see MAC_instructions_DCProgs.pdf file) have been compiled by [Andrew Plested] (http://www.fmp-berlin.info/research/molecular-physiology-and-cell-biology/research-groups/plested/mnb0.html), who has kindly agreed to help if you have problems.

Here follows short description of DOS DCprogs. For more details see [OneMol.org page] (http://www.onemol.org.uk/?page_id=331).

SCAN (DOS only!)

SCAN is ‘idealisation’ program which uses time course fitting to measure open and shut time intervals of single channel records. It converts a raw single channel recording into a list of shut times, open times and amplitudes (a .scn file) that is used for subsequent analyses.

HJCFIT

HJCFIT is a program for maximum likelihood fitting of a mechanism directly to the entire sequence of open and shut times, with exact missed events correction. The input for HJCFIT is a list of idealised open and shut time intervals. A kinetic mechanism is specified with some initial guesses for the rate constants. Currently fitting is done using the Simplex algorithm to maximise the likelihood.

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). The properties of the estimates of rate constants obtained by this method have now been evaluated (Colquhoun, Hatton & Hawkes, 2003).

EKDIST

EKDIST is used for fitting of many sorts of distributions to the output from SCAN. It fits mixtures of exponential distributions to dwell time, mixtures of geometric distributions to discrete distributions (such as the number of apparent openings per burst), and mixtures of gaussians to amplitude distributions. EKDIST also does stability plots (for amplitudes and durations), many sorts of burst analysis, subconductance transition listing (and 3D plotting), correlations of various types, including 3D bivariate distributions and dependency plots. It has far more options than any commercial program for the empirical fitting of single channel data.