Computational Biology

Standard Program for the Sc.B. Degree
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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 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.

ScB Program Requirements

Prerequisites - Students must take all of the following courses.

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

General Core Course Requirements

Chemistry
  • Equilibrium, Rate, Structure (CHEM 0330)
Biology
  • Genetics (BIOL 0470) - Prerequisite BIOL 0200 or equivalent

and select one of the following courses.

  • Introduction to Biochemistry (BIOL 0280)
  • Introduction to Cell and Molecular Biology (BIOL 0500)
Computer Science
  • (CSCI 0150) Introduction to Object-Oriented Programming and Computer Science
  • (CSCI 0160) Algorithms and Data Structures  - Prerequsite CSCI 0150

    or
  • (CSCI 0170) Computer Science: An Integrated Approach Part I
  • (CSCI 0180) Computer Science: An Integrated Approach Part II- Prerequisite (CSCI 0170)

    or
  • (CSCI 0190) Programming with Data Structures and Algorithms
  • Plus, either CSCI 0180, 0320, 0330, 0510 or any 1000-level course

    All students must take the following course:

  • (CSCI 0220) Introduction to Discrete Strucures and Probability)

    Probability and Statistics:


  • (APMA 1650) Statistical Inference I
    or
  • (CSCI 1450) Introduction to Probability and Grouping
    or
  • (MATH 1610) Probability

Computational Biology Core Course Requirements

  • (CSCI 1810) Computational Molecular Biology
  • (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 project.

PROGRAM TRACKS

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

Computational Genomics Track

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

Students are required to select three from the following.

  • Introduction to Computer Graphics (CSCI 1230)
  • Database Management Systems (CSCI 1270)
  • Introduction to Artificial Intelligence (CSCI 1410)
  • Probabilistic Methods in Computer Science (CSCI 1550)
  • Design and Analysis of Algorithms (CSCI 1570) or other Computer Science courses approved by the concentration advisor

Students must also choose three from the following.

  • Introduction to Computer Systems (CSCI 0330)
  • Introduction to Software Engineering (CSCI 0320)
  • Algorithmic Foundations of Computational Biology (CSCI 1820)
  • Statistical Methods in Bioinformatics (PHP 2620)
  • Statistical Inference II (APMA 1660)
  • Computational Theory of Molecular Evolution (BIOL 1430)
  • Human Population Genomics (BIOL 1465)

Biological Sciences Track

 

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

Students are required to select four courses comprising a coherent theme in one of the following areas.
  • Biochemistry
  • Ecology
  • Evolution/Genetics
  • Neurobiology
  • Developmental Biology
  • Immunology
  • Molecular Biology
  • Pharmacology
  • Physiology
Students must also choose two courses from the following.
  • Algorithmic Foundations of Computational Biology (CSCI 1820)
  • Statistical Methods in Bioinformatics (PHP 2620)
  • Statistical Inference II (APMA 1660)
  • Computational Theory of Molecular Evolution (BIOL 1430)
  • Human Population Genomics (BIOL 1465)

Molecular Modeling Track  

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

Students are required to take the following course.

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

Students are required to select at least three of the following.

  • Thermodynamics and Statistical Mechanics (CHEM 1150)
  • Bio-organic Chemistry (CHEM 1230), or Biochemistry (CHEM 1240), or Advanced Biochemistry (BIOL 1270)
  • Immunology (BIOL 0530)
  • Physiological Pharmacology (BIOL 1260)
  • Molecular Genetics (BIOL 1540)

Students must also choose two courses from the following.

  • Algorithmic Foundations of Computational Biology (CSCI 1820)
  • Statistical Methods in Bioinformatics (PHP 2620)
  • Statistical Inference II (APMA 1660)
  • Computational Theory of Molecular Evolution (BIOL 1430)
  • Human Population Genomics (BIOL 1465)

Applied Mathematics and Statistical Genomics Track

This Applied Mathematics and Statistical Genomics 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 the advisor is permitted.

Students must choose three courses from the following.

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

Students must also choose at least three of the following:

  • Computational Theory of Molecular Evolution (BIOL 1430)
  • Algorithmic Foundations of Computational Biology (CSCI 1820)
  • Statistical Methods in Bioinformatics (PHP 2620)
  • Quantitative Models in Biological Systems (APMA 1070)
  • Human Population Genomics (BIOL 1465)