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Bacterial Growth Curves

Lennon Lab Growth Curve Analysis Scripts

The code contained in the repo provides an anlaysis pipeline for bacterial growth curves. The code fits a Modified Gompertz Equation to optical density readings. The code uses grid searching maximum likelihood estimation to fit the model.

How to use this code

  1. Copy the contents of bin into your project
  2. Use test.example.R as a template for your analysis
  3. Proceed with analysis

Please do not save your own data to this repo

Repo Contents

bin

  • modified_Gomp.R: function for analysis pipeline
  • read.synergy.R: contains code for parsing raw data from synergy MX
  • grid.mle2.R: contains code to grid search maximum likelihood
  • curve_fit_fxs.R: contains the growth model equations

data

  • Various raw data examples

test

  • test.example.R: A script with example code

Contributors

Mario Muscarella: Ph.D. candidate in the Lennon Lab.

Dr. Jay Lennon: Principle Investigator, Associate Professor, Department of Biology, Indiana University, Bloomington. Head of the Lennon Lab.

Venus Kuo: Ph.D. student in the Lennon Lab.

License

Please see LICENSE.md