# Course Materials

- Syllabus - contains information on class times, staff, course material, course format, collaboration policy, and most other course information.
- Piazza - mandatory as this is how major announcements/homework updates will be conveyed to the class.
- Collaboration policy
- Python Primer
- Homework Guidelines
- Midterm Summary

# Original Papers

- The Markov Chain Monte Carlo Revolution
- Metropolis, Monte Carlo, and the MANIAC
- The Beginning of the Monte Carlo Method
- Metropolis Original Paper
- A structure for Deoxyribose Nucleic Acid (Watson and Crick, 1953)
- Basic Local Alignment Search Tool (Altschul, 1990)
- Info theory and substitution matrices 1992 (Altschul, 1992)
- Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes (Karlin and Altshul, 1990)
- Identification of Common Molecular Subsequences (Smith and Waterman, 1981)
- BLAST Paper
- A Model of Evolutionary Change in Proteins (Dayhoff, 1978)
- Idury-Waterman Algorithm (Idury and Waterman, 1995)
- Whole-genome shotgun assembly and comparison of human genome assemblies (Istrail et al., 2004)
- The Sequence of the Human Genome (Venter et al., 2001)

# Background Reading

- Optional textbook (also available for free online through the Brown Library)
- NCBI's Molecular Biology Review
- Introduction to Alignment Scoring Statistics

# Neat Online Demos

# Mathematica Demos

- Play with alignment! Evaluate the notebook and then move the match, mismatch, and gap penalty sliders to see how the parameters affect the output.
- Play with lander-waterman statistics and genome assembly! You'll have to enter a new name for the file location of the fasta file where the genome to be assembled is stored.

# Frequently Asked Questions

- What programming language is used in this course?
- Who takes the course?
- What biology background is needed?
- What computer science and mathematics background is needed?
- What programming background is needed?

Given that CS1810 is a requirement for the course, Python must be used for all programming assignments. Please use the Python Primer found in the Assignments section of the website to brush up on your Python!

This class is open to biologists and computer scientists, applied mathematicians, undergrads and grad students alike, as long as you have taken CS1810. As an interdisciplinary course, CS1820 attracts a diverse group of students. Past students have ranged from sophomores concentrating in Computer Science and Computational Biology through Ph.D. students in Computer Science, Applied Mathematics, and Biology.

There are no biology prerequisites, and no prior biology knowledge is assumed; the material that you need to know will be covered in class or through primers given by TAs.

CS1810 is the official requirement of the course, so students should be comfortable with programming. Students also generally have some prior exposure to basic concepts of discrete math (graphs, recurrent relations), discrete probability (random variables, independence), and algorithms (big-O notation, pseudocode).

There will be multiple programming assignments in the course, so students should have some programming background.