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---
title: "Biology 6100 - Computational Biology"
author: "Nicholas J. Gotelli"
date: "Spring 2024"
output:
prettydoc::html_pretty:
theme: hpstr
highlight: github
---
Click here for [COMPLETE SET OF PANDEMIC-YEAR COURSE VIDEOS](https://ngotelli.github.io/Bio381Vids/)
This site contains course materials, scripts, homeworks, and resources for Computational Biology, Spring 2024.
## Course Materials
[Software Installation](CourseMaterials/SoftwareInstallation.html)
[Course Syllabus](CourseMaterials/CourseSyllabus.html)
[R Scripts](Scripts/RScripts.html)
[Example Datasets](Datasets/Example_Datasets.html)
[Cheat Sheets & Programming Resources](CheatSheets/CheatSheets.html)
___
## Lecture Outlines & Homework Assignments
Date | Lecture | Homework
------------- |----------- | -------------
January 16 | [Introduction](Lectures/Introduction.html) | -
January 17 | - | [Homework #1](Homeworks/Homework_01.html)
January 18 | [GitHub](Lectures/GitHub.html) | -
January 23 | [Markdown](Lectures/Markdown.html) | -
January 24 | - | [Homework #2](Homeworks/Homework_02.html)
January 25 | [Markdown II](Lectures/Markdown.html) | -
January 30 | [Regular Expressions](Lectures/RegularExpressions.html) | -
January 31 | - | [Homework #3](Homeworks/Homework_03.html)
February 1 | [Atomic Vectors I](Lectures/AtomicVectors_I.html) | -
February 6 | [Atomic Vectors II](Lectures/AtomicVectors_II.html) | -
February 7 | **Portfolio Check #1** | [Homework #4](Homeworks/Homework_04.html)
February 8 | [Atomic Vectors II](Lectures/AtomicVectors_II.html)| -
February 13 | [Matrices, Lists, Data Frames](Lectures/MatricesListsDataFrames.html) | -
February 14 | - | [Homework #5](Homeworks/Homework_05.html)
February 15 | [Matrices, Lists, Data Frames II](Lectures/MatricesListsDataFrames.html) | -
February 20 | [Probability Distributions](Lectures/ProbabilityDistributions.html)| -
February 21 | - | [Homework # 6](Homeworks/Homework_06.html)
February 22 | [Data Curation](Lectures/DataCuration.html)| -
February 27 |[Functions](Lectures/Functions.html) | [(Experimental Designs)](Lectures/ExperimentalDesigns.html)
February 28 | | [Homework # 7](Homeworks/Homework_08.html)
February 29 | [Functions 2](https://ngotelli.github.io/Bio381Vids/) | Lecture 13
March 5 | Town Meeting Day Recess | -
March 6 | **Portfolio Check #2** | [Catch-Up Day](Homeworks/???)
March 7 | [Control Structures I](Lectures/ControlStructures_I.html)| -
March 12 | Spring Recess | -
March 13 | Spring Recess | -
March 14 | Spring Recess | -
March 19 | [dplyr/SQL](Lectures/dplyr_Lecture1.html)| -
March 20 | [dplyr+SQL lecture notes](Lectures/dplyr_SQL_Lecture.html) | [Homework #8](Homeworks/Homework_06a.html)
March 21 | [For Loops I](Lectures/ForLoops_I.html) | -
March 26 | [For Loops II](Lectures/ForLoops_II.html) | -
March 27 | - | [Homework #9](Homeworks/Homework_09.html)
March 28 | [Strategic Coding Practices I](CourseMaterials/StrategicCodingPractices.zip) | -
April 2 | [Strategic Coding Practices II](CourseMaterials/StrategicCodingPractices.zip) | -
April 3 | - | [Homework #10](Homeworks/Homework_10.html)
April 4 | [ggplot I](Lectures/ggplot_I.html) | -
April 9 | [ggplot II](Lectures/ggplot_II.html) | -
April 10 | **Portfolio Check #3** | [Homework #11](Homeworks/Homework_11.html)
April 11 | [ggplot III](Lectures/ggplot_III.html) | -
April 16 | [ggplot IV](Lectures/ggplot_III.html) | -
April 17 | - | [Homework #12](Homeworks/Homework_12.html)
April 18 | [Functional Programming](Lectures/Lecture_24.xhtml) | -
April 23 | [Shell Commands](Lectures/Lecture25_S2021.xhtml) | -
April 24 | - | Catch-up Day
April 25 | - | Catch-up Day
April 30 | Lecture Spillover Day | -
May 1 | Lecture Spillover Day | -
May 2 | Lecture Spillover Day | -
___
### Important Dates
- 22 January: Last day to add classes without instructor permission
- 29 January: Add/Drop, Pass/No Pass, Audit Deadline
- 1 April: Last day to withdraw
- 19 April: Honors Day
- 3 May: Last day of classes
- 4,5,8 May: Reading days
- 6,7,9,10 May: Final exam days
___
### Meet The Class of 2024
Student | GitHub and Portfolio Links | Fun Fact
------------- | -------------- | -------------
Carlos Amissah | [GitHub](https://github.com/carlosamissah) [Portfolio](https://carlosamissah.github.io/try-again/) | I love Ghana jollof
Anushka Canfield | [GitHub](https://github.com/ACanfield7) [Portfolio](https://acanfield7.github.io/CanfieldBiol6100) | I don't know the day I was born. My birthdate is an educated guess.
Emily Dombrowski | [GitHub](https://github.com/emilydombrowski) [Portfolio](https://emilydombrowski.github.io/comp_bio_24/) | I have a pug named Penelope!!!
Madelynn Edwards | [GitHub](https://github.com/Medwards13) [Portfolio](https://medwards13.github.io/EdwardsBIO6100/) | I love bugs!
Gwen Ellis | [GitHub](https://github.com/g-ellis) [Portfolio](https://g-ellis.github.io/Bio6100) | I was a junior Olympian in cross country!
Nicole Gorman | [GitHub](https://github.com/NicoleRGorman) [Portfolio](https://nicolergorman.github.io/ComputationalBiology) | My favorite movie is Shawshank Redemption.
Nick Gotelli | [GitHub](https://github.com/GotelliLab) [Portfolio](http://www.uvm.edu/~ngotelli/homepage.html) | For the past 40 years, I have owned and raised pure-bred, show-quality chow chows.
Kyle Grasso | [GitHub](https://github.com/KyleGrasso) [Portfolio](https://kylegrasso.github.io/GrassoBio6100) | I can solve a Rubik's Cube and I also know how to juggle. Unfortunately, I can't do both at the same time.
Rachel Hall | [Github](https://github.com/rachelkhall) [Portfolio](https://rachelkhall.github.io/Bio6100) | I am from Charlotte, North Carolina and my undergrad was at NC State University studying Textile Engineering with a minor in Chemical Engineering.
Chika Ikpechukwu | [GitHub](https://github.com/cikpechu) [Portfolio](https://cikpechu.github.io/ComputationalBiology/) | I love dancing
Alexander Kissonergis | [GitHub](https://github.com/beatlesnstuff) [Portfolio](https://beetlesnstuff.github.io/computationalBiology/) | I enjoy climbing.
Teresa Mungazi | [GitHub](https://github.com/EconTerrie) [Portfolio](https://econterrie.github.io/MungaziBio6100) |
George Ni | [GitHub](https://github.com/georgeni2442) [Portfolio](https://georgeni2442.github.io/TestRepo) | I used to train birds for falconry and science shows.
Maryam Nouri-Aiin | [GitHub](https://github.com/Maryam-Nouri-Aiin) [Portfolio](https://maryam-nouriaiin.github.io/NouriAiinBio381) | my house plants :)
Megan O'Connor| [GitHub](https://github.com/meganeoc) [Portfolio](https://meganeoc.github.io/O-Connor_Biol6100/) | When I interned at an aquarium I got to take care of/hang out with an octopus named Pepper!
Frances Oppenheimer | [GitHub](https://github.com/FOpp14) [Portfolio](https://fopp14.github.io/OppenheimerBio6100/) | I'm the director of punk music at WRUV
Daniel Penados-Richter | [GitHub](https://github.com/DanielPR23) [Portfolio](https://danielpr23.github.io/DanielPenadosBio6100/) | I like to cook. My grill chicken is particularly good!
Nicole Phelan | [GitHub](https://github.com/nicolephelan) [Portfolio](https://nicolephelan.github.io/PhelanBIOL6100) | During my free time I like to bake
Molly Ratliff | [GitHub](https://github.com/maratlif) [Portfolio](https://maratlif.github.io/RatliffBio6100) | I am from Michigan
Ely Remes | [GitHub](https://github.com/Ely-Remes) [Portfolio](https://ely-remes.github.io/RemesBiol6100/) | I teach skiing
Chanchal Saratkar | [GitHub](https://github.com/csaratkar) [Portfolio](https://csaratkar.github.io/SaratkarBio6100) | I like to collect animal specimens.
Shelby Scarfo | [GitHub](https://github.com/ShelbySarfo) [Portfolio](https://shelbyscarfo.github.io/ScarfoBio6100Portfolio/) | I have lived in every state in New England.
Jenner Smith | [GitHub](https://github.com/mjennersmith)[Portfolio](https://mjennersmith.github.io/BIO6100)|
Kelsey Soule | [GitHub](https://github.com/kelseysoule) [Portfolio](https://kelseysoule.github.io/SouleComputationalBiology/) | My favorite ice cream flavor is banana.
Alexander Steiner | [GitHub](https://github.com/aksteiner) [Portfolio](https://github.com/aksteiner/SteinerBio381) | I am an identical twin.