Data Sets

Measuring Bacterial Growth  A series of fluorescence and phase contrast images of E. coli cells growing on a rich medium substrate.

Testing The French Flag Model Brightfield images of developing Drosophila embryos with different dosages of the Bicoid morphogen. Also download a
csv
file containing more dosages from Thomas Gregor. 
Example Images lacI titration  Example brightfield and fluorescence images of E. coli cells for the gene expression measurement analysis.

LacI Titration  Brightfield and fluorescence images of E. coli cells containing different numbers of transcriptional repressor molecules. Also download the
.csv
file of foldchange data from Garcia and Phillips 2011. 
Measuring Cytoskeletal Filament Length Distributions  Fluorescence images of actin filaments prepared in vitro during Physiology 2016.

Timing Transcription in Drosophila  This data set from Hernan Garcia’s lab contains images from two developing Drosophila embryos in which either the 5’ or 3’ end of the hunchback morphogen mRNA is labeled with MS2.
Exercises
The code we write in class will be added here as the course progresses.

Integrating Cell Division by the Euler Method  Here, we get introduced to the MATLAB programming language and learn how to numerically solve the differential growth equation. pdf

How the Fly Gets Its Neck  In this tutorial we go through the theory and analysis of the cephalic furrow positioning in the fly embryo. html  mlx

Measuring Growth Rate Through Microscopy  We’ve all (probably) measured bacterial growth by recording the OD of growing cultures. In this script, we analyze a timelapse microscopy data set by measuring the bacterial area as a function of time.  inclass code  data set

Timing Transcription in Drosophila embryos  Using some of the image processing skill we learned while processing the growth movie, we measure the rate of transcription of the hunchback gene. html  mlx

Nonlinear Regression  We performed a nonlinear regression of our LacI titration data to estimate the best fit value for the binding energy of a repressor to the DNA.

Cytoskeleton length distribution  Data analysis of cytoskeleton images to obtain the length distribution and compare it with the theoretical predictions from the chemical master equation model. html  mlx
Advance Matlab tutorial (introduction to Bayesian inference)

Intro to Bayesian inference  First exposition to the concept of Bayesian parameter inference. [ html ]  [ mlx ]  [ raw data ]

Intro to Markov Chain Monte Carlo sampling  Introduction to the powerful MCMC techniques widely used for Bayesian analysis. [ html ]  [ mlx ]
Extra Tutorials
We have written several more indepth tutorials on programming in the MATLAB programming language and have posted them below. More will be posted as the course progresses.

Intro to Matlab and Sizing Up E. coli  This tutorial will teach some basics of the MATLAB programming language as well as developing a feeling for the size of E. coli cells. [data set ]

Numerical Integration Of Bacterial Growth  This tutorial covers how to solve differential equations numerically.
External Resources
Below is a list of useful online resources for learning the some principles of programming and scientific data analysis using the Python language.