Length control

Overview

This page describes how to analyze length control experiments (the sort where you include stretches and/or k_tr measurements)

Here’s the big picture:

• Analyze all of your data to create a single Excel file that contains many parameters (for example, force, stiffness, k_tr) for every SLControl record you collected.
  • We call that file the raw_lc_analysis_file
• Parse the raw_lc_analysis_file to extract data for certain conditions (e.g. records at a certain pH).
• When you extract this data, keep track of which files contain data from each preparation and use that information to calculate things like relative tension and pCa₅₀ that require comparing data from multiple files.
  • The file containing the extracted data is the processed_lc_analysis_file

Strong recommendation

Run your analysis incrementally until you get the hang of it because it is relatively easy to troubleshoot an analysis that only includes a few files, and quite challenging to troubleshoot a large project.

To run incrementally:

• Test your analysis for each preparation by itself
  • Create a test folder structure that only contains data from one preparation
  • Analyze that folder to create a raw_lc_analysis_file
  • Run your extracts on that folder and create a processed_lc_analysis_file.
  • Make sure you understand the output and that it makes experimental sense
  • If you encounter problems, a common source of error is incorrect metadata in the SLControl files. Check that first.
• Then repeat the process replacing the data in your test folder with data from the next preparation.
• Keep going until you are confident that each preparation produces satisfactory output.
• Finally, run your analysis starting with the top level data folder.

Workflow

• Organize your data
• Update your repositories. You need the latest versions of
  • SLControl analysis
  • SLControl utilities
  • MATLAB utilities
• Make sure all of these repositories are on your MATLAB path
• Start MATLAB
  • Change the working directory to <SLControl_analysis_repo>/code/analysis_gui.m
  • Press F5 to get this window

• Start with the top left panel Analyse length control *.slc files
  • Set the top data folder (the folder that contains all the files and folders you want to analyze - though remember the Strong recommendation above as you are getting started)
  • Set the analysis file (where you want to store the raw_lc_analysis_file)
  • Use include_string and exclude_string to confine your search to certain files in the directory
    • you may not have to use these options, in which case leave them as is
  • Press

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