# The Comp Bio Major This document provides guidance for Computational Biology majors and their advisors. Information on the major in [Biology is available separately](https://hackmd.io/@aphanotus/BioMajorChecklist). From the college [catalog](https://www.colby.edu/catalogue/): > The major in computational biology allows students to develop a coherent plan for the integration of computer science with biology. Students completing this major will be well prepared to obtain employment or pursue research in fields such as computational biology and bioinformatics. ----- ## Major requirements Students will design an integrative course of study in collaboration with academic advisors from the Biology and Computer Science departments. It is each student's responsibility to make sure they meet major requirements. Faculty act as advisors only. ### Required core courses These eleven courses provided foundational skills and introduce concepts that are central to computational biology. Foundational courses (100-level) may be satisfied by AP or other placement exams. _(* Requirements added for students declaring the major in Academic Year 2020-2021 and beyond.)_ | course number | course name | language | | -------------- | ------------- | -------------- | | [BI163](https://aphanotus.github.io/openEd/BI163.22F.CellularBasisOfLife/) | The Cellular Basis of Life | R | | [BI164](https://aphanotus.github.io/openEd/BI164.23S.Evolution.and.Diversity/) ^a^ | Evolution and Diversity | R | | CS151, CS152, CS153, CS154 or CS166 ^b^ | [Computational Thinking](https://cs.colby.edu/index.php) | python | | MA121 | Single variable [Calculus](https://www.colby.edu/academics/departments-and-programs/mathematics/academic-program/calculus-courses/) | | | MA122 * | Multivariable Calculus | | | [BI278](https://web.colby.edu/noh-lab/bi278-introduction-to-genomics/) | Genomics | Unix, R | | BI279 | Genetics | R | | [CS231](http://cs.colby.edu/courses/S19/cs231/) | Data Structures and Algorithms | java | | [CS251 or CS252](http://cs.colby.edu/courses/S19/cs251/) | Data Analysis and Visualization | python | | MA253 * or [MA262](http://personal.colby.edu/personal/s/sataylor/teaching/S12/MA262/MA262Resources.php) * ^c^ | Linear Algebra or Vector Calculus | | | [SC212](https://libguides.colby.edu/SC212) | Intro to Statistics | R | ### Elective courses at the 300-level or above, two each in Biology* and Computer Science These courses demonstrate areas of application for computational biology represented at Colby. Below are recommended courses, and other courses may be approved in advance in consultation with the student's major advisor. Be aware that 300-level courses can have prerequisites that are not part of the Comp Bio core curriculum. _(* Students who declared the major prior to academic year 2020-2021 are required to take one biology course from this list or another approved by their advisor.)_ | course number | course name | language | | -------------- | ------------- | -------------- | | BI320 | Evolutionary Analysis | | | BI323 | Plant Genetic Engineering | | | [BI345](https://web.colby.edu/noh-lab/bi345-advanced-genomics/) | Advanced Genomics | Unix, R | | BI351 | Applied and Environmental Microbiology | | | BI371J | Applied Biomedical Genomics | | | BI376 | Development, Genes, and Evolution | | | BI378 | Molecular Biology | | | [BI382](https://colbyecology.github.io/) | Ecological Modeling | R | | [CS341](https://cs.colby.edu/courses/F20/cs341/syllabus.php) | Systems Biology I | MatLab | | [CS441](https://cs.colby.edu/courses/S23/cs441/syllabus.php) | Systems Biology II | MatLab | | [CS343](https://cs.colby.edu/courses/F20/cs343/) | Neural Networks | python, MatLab | | [CS443](https://cs.colby.edu/courses/S20/cs443/) | Computational Neuroscience | python, MatLab | | [CS346](https://cs.colby.edu/courses/S20/cs346/) | Computational Modeling and Simulation I | python, MatLab | | [CS446](https://cs.colby.edu/courses/F20/cs446/) | Computational Modeling and Simulation II | python, MatLab | ### Notes ^a^ These courses fulfill the intro Bio requirement and will form your foundation for college-level scientific experimentation and writing. ^b^ These courses that fulfill the intro CS requirement differ primarily in their project theme. Students are free to choose which ever they prefer, but CS152 may be most generally useful. The project in CS151 deals with graphics; CS152 focuses on science. These two courses teach python. (CS153 fulfills this requirement, but will not likely be offered in the foreseeable future.) ^c^ Depending on their area of interest, Comp Bio majors should choose one or the other. MA253 is recommended for most students, and especially those with an interest in Genomics. MA262 may be preferable for students with an interest in modeling physical biological systems or interactions. If students find that they are interested in additional Statistics courses, we recommend SC321 (Statistical Modelling) or SC397 (Statistical Learning). ## Miscellanous - **Internship** credits will not count toward major requirements. - **Off-campus study (OCS)**: Courses taken off-campus must be approved by the OCS office for transfer of credits to Colby. There is a limit of 8 credit hours that can be tranferred to Colby from most OCS programs. For an OCS course to count towards a major requirement it must be approved by the department chair or OCS liaison in the appropriate department. (Biology courses are approved by the Biology department; Chemistry courses by the Chem Dept; etc.) However, grades for OCS courses do not contribute to Colby GPA. - There are **exceptions to these OCS rules**. For example, the [Bigelow Semester Program](https://life.colby.edu/offcampus/colby-at-bigelow-laboratory/) provides 16 credits in Chemistry, ES and Biology. - **Double majors or minors**: You cannot do a double major or minor with Comp Bio and Data Science. No "Computational XXX" majors are allowed to do this. You are allowed to double major or minor in Bio (only major), CS, or Stats. --- ## Links - [Colby Biology](http://www.colby.edu/bio/) - [Colby CS](https://cs.colby.edu/) - [Colby Math & Stats](http://www.colby.edu/mathstats/)
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Dave Angelini
Associate professor of genetics at Colby College, interested in alternative developmental outcomes, e.g. serial homology, sexual dimorphism and polyphenism.
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Colby Biology Information

Biology major requirements

4/15/2024
The Biology Major Checklist

This document provides guidance for Biology majors and their advisors. Updated 14 November 2022, for classes matriculating Fall 2020 and onwards. Information on the major in Computational Biology is available separately.

4/11/2024
R Tutorial

BI376 For the week of 14 September 2020 Rmd version of this script Tutorial instructions The final project for BI376 this semester will employ morphometric analysis in R, a free platform for statistical computing. While you've probably encountered R in other courses, this tutorial is meant as a refresher and as a reference. Later lab protocols will provide information on how you can explore more advanced features. While I hope you will look through all of this document, some of the material may be familiar and some may be new. At the end, there is a brief exercise asking you to send in a demonstration of your R skills.

2/22/2024
Bread Notes

Link to untested Bread Ideas :::info General tips Start the yeast. For any recipe using dry yeast, mix the yeast with warm water (110-115˚F) and about 1 teaspoon of honey. Let it stand for 5-10 min, until foamy. This will activate the yeast. In any recipe, it's possible to substitute sourdough starter for flour and water. For example 100 g of starter can replace 50 g water and 50 g flour. Be sure to keep at least 50 g of water in the recipt to start the yeast-- and it does seem wise to keep at least some dried yeast in the bake. In our convection oven, it's always necessary to cover bread to prevent the top from burning. Place a bread pan in the air frying basket on the bottom rung to maximize its head space. :::

12/23/2022
Read more from Dave Angelini
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