Tutorials
We will have several computational tutorials throughout the course. As the course progresses, these materials will be posted below. Note: In some browsers (Firefox primarily), the end of each sentence is clipped off, making it difficult to read. If this is occurring, please try using another browser (Chrome, Safari, etc).
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Tutorial 0a Setting up Python | This tutorial will walk you through how to install a Python 3.8 scientific computing environment.
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Using the Jupyter notebook | This tutorial will teach you how to write code and text in Jupyter notebooks for homework submissions.
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A Primer on Python Syntax | This tutorial will walk you through the basics of programming in Python.
Syllabus for Computational Sessions and Datasets
We introduce you to several techniques, such as numerical integration, image segmentation plotting with dashboards. Please download the following data sets, unzip them, and place them in your bootcamp/data folder as described in the setting up Python tutorial. Depending on the browser, you can download the data by left-clicking the link, or by right-clicking the link, and select Save link as. The following syllabus is subject to change and will be kept in line with the class:
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Day 1: Exponential growth and numerical integration | Notebook
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Day 2: Image analysis of virion particles | Electron microscopy images of Sars-Cov2 virions | Notebook from class | Notebook with edge detection
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Day 3: Exponential growth revisited with microscopy | Set of phase contrast and fluorescence images of a growing E. coli. colony | Notebook
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Day 4: Spread the butter | Notebook
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Day 5: Probability distributions of mRNA counts in yeast | Mdn1 and Pdr5, adapted from this paper. | Notebook 1 | Notebook 2
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Day 6: Using sequencing to quantitatively measure gene regulation.| Data set
Exercises
As we progress through the course, the code written in class will be posted here, along with the polished version of the same material.
External resources
Below is a list of useful online resources for learning the Python programming language and principles of programming in general.
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Probability Distribution Explorer by Justin Bois | Explains various probability distributions and their stories.