https://github.com/mathworks-teaching-resources/biosciences-genetics
This is an interactive courseware module for use in introductory biology classrooms. This module teaches the basics of genetics using biological real datasets. It includes several live scripts.
https://github.com/mathworks-teaching-resources/biosciences-genetics
Last synced: over 1 year ago
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This is an interactive courseware module for use in introductory biology classrooms. This module teaches the basics of genetics using biological real datasets. It includes several live scripts.
- Host: GitHub
- URL: https://github.com/mathworks-teaching-resources/biosciences-genetics
- Owner: MathWorks-Teaching-Resources
- License: other
- Created: 2024-04-16T19:47:10.000Z (about 2 years ago)
- Default Branch: release
- Last Pushed: 2024-04-30T13:31:28.000Z (about 2 years ago)
- Last Synced: 2025-01-23T17:57:28.968Z (over 1 year ago)
- Language: MATLAB
- Size: 27.1 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: license.txt
- Security: SECURITY.md
Awesome Lists containing this project
README
# Biosciences: Genetics
[](https://www.mathworks.com/matlabcentral/fileexchange/163706-biosciences-genetics) or
[](https://matlab.mathworks.com/open/github/v1?repo=MathWorks-Teaching-Resources/biosciences-genetics&file=S1_Introduction.mlx)
This curriculum module teaches students the basic concepts involved in computational genetics.
## Description
In this module, we will learn how to use MATLAB to analyze genetic data. We will calculate the statistics of a single DNA sequence, use real genetic data to create a phylogenetic tree, and explore within-species genetic variation. Make sure you're familiar with the basics of using MATLAB by going through the [MATLAB Onramp](https://matlabacademy.mathworks.com/details/matlab-onramp/gettingstarted) before continuing.
This module utilizes data pulled from [GenBank](https://www.ncbi.nlm.nih.gov/genbank/), the NIH's library of publicly available genetic sequences.
[A 3-dimensional model of DNA](https://commons.wikimedia.org/wiki/File:Bdna_cropped.gif)
## Prerequisites
This module assumes basic MATLAB knowledge and it is recommended that all students take the [MATLAB Onramp](https://matlabacademy.mathworks.com/details/matlab-onramp/gettingstarted).
## Getting Started
To learn more about opening and using MATLAB, see the accompanying [Getting Started](Getting_Started.pdf) guide.
## Sections
Notes: These scripts can all be run independently, though we recommend going through these live scripts in order. These live scripts are intended to be used with output inline. To change the output, go to the View tab of the toolstrip, and select  Output Inline.
The scripts have areas for the students to interact with the code  . There will also be exercises  in most scripts and the answers will be provided at the end. A problem set for students to practice these concepts is also included here. Throughout the scripts, there are also moments to students to reflect on what they've learned or on what the data means  . Particularly interesting examples of how these concepts are used in "real-world" biology are also pointed out .
[Introduction](https://matlab.mathworks.com/open/github/v1?repo=MathWorks-Teaching-Resources/biosciences-genetics&file=S1_Introduction.mlx)
- Learning objective: Students will learn about how computation is used in genetics.
[Explore a single DNA sequence](https://matlab.mathworks.com/open/github/v1?repo=MathWorks-Teaching-Resources/biosciences-genetics&file=S2_Single_seq.mlx)
- Learning objective: Students will learn to import and analyze DNA sequences in MATLAB, and visualize nucleotide content.
[Comparative genetics](https://matlab.mathworks.com/open/github/v1?repo=MathWorks-Teaching-Resources/biosciences-genetics&file=S3_Comparative_genetics.mlx)
- Learning objective: Students will calculate genetic distances between species, visualize genetic distance using phylogenetic trees, and use the data to interpret evolutionary relationships.
[Population genetics](https://matlab.mathworks.com/open/github/v1?repo=MathWorks-Teaching-Resources/biosciences-genetics&file=S4_Population_genetics.mlx)
- Learning objective: Students will visualize genetic differences within a population using dimensionality reduction.
[Problem set](https://matlab.mathworks.com/open/github/v1?repo=MathWorks-Teaching-Resources/biosciences-genetics&file=S5_Problem_set.mlx)
- [Problem set answers](https://matlab.mathworks.com/open/github/v1?repo=MathWorks-Teaching-Resources/biosciences-genetics&file=S6_Problem_set_answers.mlx)
## Related Courseware Modules
Link to 5 other modules here once set up.
## Products
MATLAB®, Bioinformatics Toolbox™, Statistics and Machine Learning Toolbox™
## License
The License for this project is in the [License.txt](license.txt) file in this repository.
##
_© Copyright 2023 The MathWorks, Inc._