Curve Fitting
for Fluorescence Intensity Transitions
and Size Exclusion Chromatograms


Differential Scanning Fluorimetry (DSF, aka Tm) Scripts

DSF (Tm) Sample Data Files

See flowchart for how these scripts and files are related.

Size Exclusion Chromatography (SEC) Script and Sample Data Files

Flowchart of DSF (Tm) Data and Processing

Source RT-PCR machine
Export and reformat if needed
Input DSF_sample_data.csv (requires Perl and gnuplot.)
Output1 DSF_sample_data.tmc.csv
Tm Shift Tables DSF_sample_data.tmc.shift.csv

1 Other output: DSF_sample_data_fit_dir.tar.gz - intermediate files, plots and web pages

File Formatting for DSF (Tm) Input Files

The script can take text files as input if they: use a consistent delimiter; have a header line with a field starting 'Tem' (for Temperature) followed by sample name fields; and have temperature and sample fluorescence intensity values in the rows following the header, in the same columns as their labels in the header.

The software available with the Opticon Monitor RT-PCR machine exports .csv files in this format, e.g. DSF_sample_data.csv. Binary files in Opticon Monitor raw data format, (extension .tad or .tad2) can be converted to this .csv format either by exporting them via Opticon Monitor 3 software, or with the perl script .

Other RT-PCR Machines: SGC Transform Spreadsheets

The script is designed to take a wide variety of formats. If you have a .csv file exported from an RT-PCR machine other than an Opticon Monitor, you should first try it directly with or on the FIT server. If it runs without error and produces plots including all the data and reasonable fits, then you can save several steps, preserve column headers and preserve data finer than one degree Celsius if you have any. If it does not run correctly, then you may be able to use one of the "Transform" spreadsheets developed by the Structural Genomics Consortium (SGC) to reformat your data. These spreadsheets produce a common format readable by either SGC's DSF analysis tool or by and the FIT server. The first step is to download the Transform appropriate for your RT-PCR machine:

Sample files and an instruction manual are available from SGC. See the DSF format documentation for the basic steps to copy and paste your data from the original spreadsheet into the first page of the transform sheet, then save the transform output as a .csv file which can read.