# Computational Biology Undergraduate Program

## Standard Program for the Sc.B. Degree

Computational biology involves the analysis and discovery of biological phenomena using computational tools, and the algorithmic design and analysis of such tools. The field is widely defined and includes foundations in computer science, applied mathematics, statistics, biochemistry, molecular biology, genetics, ecology, evolution, anatomy, neuroscience, and visualization.

Our program educates the student liberally in these fields, building on a foundation of coursework that may then focus via several possible tracks. The program offers four possible tracks: computational genomics, biological sciences, molecular modeling and applied mathematics and statistical genomics. The program requires a senior capstone experience that pairs students and faculty in creative research collaborations.

Computational Biology graduates are candidates for competitive positions in industry or for training in academic science

### Prerequisites

- MATH 0100 (Introductory Calculus II) or MATH 0170 (Advanced Placement Calculus)
- BIOL 0200 (The Foundation of Living Systems)

or equivalents

### General Core Course Requirements

*Chemistry:*

- CHEM 0330 (Equilibrium, Rate, Structure)

*Biology:*

- BIOL 0470 (Genetics) Prerequisite BIOL 0200 or equivalent

and one of the following: - BIOL 0280 (Introduction to Biochemistry)
- BIOL 0500 (Molecular Cell Biology)

*Computer Science:*

- CSCI 0150 (Intro to Object-Oriented Programming & Computer Science) No Prerequisite
- CSCI 0160 (Algorithms and Data Structures) Prerequisite CSCI 0150

or

- CSCI 0170 (Computer Science: An Integrated Introduction Part I) No Prerequisite
- CSCI 0180 (Computer Science: An Integrated Introduction Part II) Prerequisite CSCI 0170

or

- CSCI0190 Programming with Data Structures and Algorithms
- CSCI0220 (Introduction to Discrete Structures and Probability) No Prerequisite

*Probability and Statistics:*

- APMA 1650 (Statistical Inference I)

### Computational Biology Core Course Requirements

- CSCI 1810 (Computational Molecular Biology) Prerequisite (CSCI 0160 or 0180) & CSCI 0220
- APMA 1080 (Statistical Inference in Molecular Biology and Genomics)

** Capstone Experience:** Students enrolled in the computational biology concentration will complete a research project in their senior year under faculty supervision. The themes of such projects evolve with the field and the technology, but should represent a synthesis of the various specialties of the program. A minimum of one semester of independent study is required (such as BIOL 1950 or CSCI 1970), although many students may conduct a full year of independent study.

** Honors:** To be a candidate for honors, a student must have a course record judged to be excellent by the concentration advisor and must complete a thesis judged to be outstanding by the faculty member supervising the work.

### Specialized Tracks

Students must complete six courses in one of the following four tracks, as specified below:

** Computational Genomics Track:** This track is designed for students whose interests lie in the development of algorithms and high-quality software (tools and systems) for biological applications.

Three of the following:

- CSCI 1230 (Introduction to Computer Graphics)
- CSCI 1270 (Database Management Systems)
- CSCI 1410 (Introduction to Artificial Intelligence)
- CSCI 1550 (Probabilistic Methods in Computer Science)
- CSCI 1570 (Design and Analysis of Algorithms)

or other CS courses approved by the concentration advisor

Three of the following:

- CSCI 0310 (Introduction to Computer Systems)
- (CSCI 0320 (Introduction to Software Engineering)or
- CSCI 0360 (Introduction to Systems Programming))
- CSCI 1950-L (Algorithmic Foundations of Computational Biology)
- PHP2620 (Statistical Methods in Bioinformatics)
- APMA 1660 (Statistical Inference II)
- BIOL 1430 (Computational Elements of Molecular Evolution)

** Biological Sciences Track:** This track is designed for students whose interests lean more towards biological questions.

At least four courses comprising a coherent theme in one of the following areas:

- Biochemistry
- Ecology
- Evolution
- Neurobiology

Two courses from the following:

- CSCI 1950-L (Algorithmic Foundations of Computational Biology)
- PHP2620 (Statistical Methods in Bioinformatics)
- APMA 1660 (Statistical Inference II)
- BIOL 1430 (Computational Elements of Molecular Evolution)

** Molecular Modeling Track:** This track is designed for students who wish to gain competence in the field of molecular modeling and drug design.

- CHEM 1220 (Computational Tools in Biochemistry and Chemical Biology)

At least three courses from the following:

- CHEM 1150 (Thermodynamics and Statistical Mechanics)
- CHEM 1230 (Chemical Biology), CHEM 1240 (Biochemistry) or BIOL 1270 (Advanced Biochemistry)
- BIOL 0530 (Principles of Immunology)
- BIOL 1260 (Physiological Pharmacology)
- BIOL 1540 (Molecular Genetics)

Two courses from the following:

- CSCI 1950-L (Algorithmic Foundations of Computational Biology)
- PHP2620 (Statistical Methods in Bioinformatics)
- APMA 1660 (Statistical Inference II)
- BIOL 1430 (Computational Elements of Molecular Evolution)

** Applied Mathematics and Statistical Genomics Track:** This track is designed for students whose interest focuses on extracting information from genomic and molecular biology data, and modeling the dynamics of these systems. Substitution of more advanced courses with consent of advisor is permitted.

At least three courses from the following:

- APMA 1660 (Statistical Inference II)
- APMA 1690 (Computational Probability and Statistics)
- CSCI 1410 (Introduction to Artificial Intelligence)
- APMA 0340 (Methods of Applied Mathematics I) {or APMA 0330}
- APMA 0360 (Methods of Applied Mathematics II) {or APMA 0350}

At least three of the following:

- BIOL 1430 (Computational Theory of Molecular Evolution)
- CSCI 1950-L (Algorithmic Foundations of Computational Biology)
- PHP2620 (Statistical Methods in Bioinformatics)
- APMA 1070 (Quantitative models in Biological Systems)