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readme.md

Demo for fitting DNA replication fraction data

Origin and usage

  • This repository contains a modified subset of the code used for Modeling genome‐wide replication kinetics reveals a mechanism for regulation of replication timing. Scott Cheng-Hsin Yang, Nicholas Rhind, and John Bechhoefer. Molecular Systems Biology 6:404 (2010).
  • The code is good for fitting time-course replication fraction.
  • Original fitting was done in Igor Pro 6 on Windows.
  • The folder FasterMicroArrayFitFunc contains an implementation of the main fitting function in c. These were used for the genome-wide fit.
  • In function fastfxt(...), the comment label "diff" marks new changes compare to original code.

Warning

  • The following instructions have been tested only for an MIM fit to fake data on Igor Pro 7.0 (Mac).

Getting started

  • Download, install, and open Igor Pro.
  • In Igor, Windows --> New --> Procedure. Copy the content of fit_microarray.txt into the procedure file. Click the Compile button.
  • In Igor, Windows --> New --> Notebook. Copy the content of fit_notes.txt into the notebook file.
  • Follow instructions in notebook.

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Demo for fitting DNA replication fraction

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