CS612: Algorithms in Bioinformatics

Fall 2020

Instructor

Name: Nurit Haspel
email: nurit.haspel@umb.edu
Office: S-3-71
Office hours: Tu, Th 12:30–2:00PM, virtually


Class meetings

Tu, Th 2:00-3:15 on Blackboard


Course Description

This course will introduce students to bioinformatics - the area concerning the development and application of computational methods to address key problems in biology. It will introduce the students to a variety of methods and skills required to conduct research in this highly rising field. The emphasis of the course is structural bioinformatics with focus on various computational methods to simulate, analyze and model protein structure, dynamics and function. Other subjects such as systems biology, genomics and interaction networks will be introduced as well. The course is designed first and foremost for computer scientists but is also open to biology majors with adequate computational/mathematical background.

See the course syllabus for a detailed list of topics.

Prerequisites: CS210 or equivalent knowledge in data structures and programming, MATH 260 (Linear algebra).


Homework assignments

Assignment (PDF) Posted/Given on Due Date Handouts Solution
Homework #1 Sep. 22, 2020 Oct. 1, 2020, on Gradescope protein.fasta
dino.fasta
Homework #2 Oct. 2, 2020 Oct. 13, 2020, on Gradescope query_hw2.fasta
Homework #3 Oct. 17, 2020 Nov. 5, 2020, on Gradescope  
Homework #4 Nov. 5, 2020 Nov. 21, 2020, on Gradescope HW4.R
Term project Oct. 26, 2020 Dec. 21, 2020
Homework #5 Nov. 29, 2020 Dec. 14, 2020

 


Class notes

Week

Topic

Book Chapters

Session Dates

Session Info

Slides/notes

1

Introduction

Tuesday,
September 8

Intro to Molecular Biology
and Bioinformatics

Introduction

Thursday,
September 10

Same

Same as last time

2

Introduction
Sequence alignment

Tuesday,
September 15

Intro
Start sequence alignment

Sequence

Thursday,
September 17

Sequence Alignment

DP notes

3

Sequence alignment

Tuesday,
September 22

Sequence alignment
MSA

Thursday,
September 24

Intro to Protein Structure

Structure

Structure notes

4

Protein Structure

Tuesday,
February 19

Protein Structure

Thursday,
February 21

Biological Databases

Databases

Databases notes

5

Visualization, Folding

Tuesday,
October 6

Protein Visualization

Visualization

Thursday,
October 8

Start folding

Folding

Folding notes

6

Folding

Tuesday,
October 13

Protein Folding

Geometric Preliminaries
Notes

Thursday,
October 15

7

Folding
Folding Methods

Tuesday,
October 20

Folding Methods

Folding methods
Folding methods notes

Thursday,
October 22

8

Folding methods
Distance measuring

Tuesday,
October 27

Folding methods

Thursday,
October 20

Distance measurement

Distance Measure

Distance notes

9

Simulations

Tuesday,
November 3

Biomolecular Simulations

Simulations
Simulations notes

Thursday,
November 5

Simulations
manipulations

See Oct. 13 notes (Geometric Prelims).

10

Structural Manipulation

Tuesday,
November 10

Thursday,
November 12

11

Structural Alignment

Tuesday,
November 17

Structural Alignment

Structural Alignment
Structural Alignment notes

Thursday,
November 19

12

Docking

Tuesday,
November 24

Docking Docking
Docking notes

Thursday,
November 26

Thanksgiving

13

Docking
Sampling

Tuesday,
December 1

Flexible Ligand
Forward kinematics

Sampling
Sampling notes

Thursday,
December 3

14

ANN
Sampling

Tuesday,
December 8

ANN demo
Sampling

ANN Demo

Thursday,
December 10


Recommended Textbooks

Structural Bioinformatics, edited by Jenny Gu and Phillip E. Bourne, Willey Blackwell, 2nd edition.

Introduction to Bioinformatics, Arthur M. Lesk, Oxford, 3rd or 4th edition.

Some course material includes modules developed as part of the connexions project by Prof. Lydia Kavraki.


Online material

All material for this course will be kept online at http://www.cs.umb.edu/~nurith/cs612.


Written work

There will be about 4-5 written homeworks, a final project and a presentation. For more information, see the syllabus.

For a list of possible topics see here. I am open to any other ideas that are in line with the course material.


Grade Composition


Honesty

You must do your own work in this course. You are encouraged to discuss problems/projects with classmates, or to ask for help with debugging. When you do share ideas or get help you must acknowledge that help in writing. However IT IS NOT ALLOWED TO USE ANOTHER STUDENTS CODE IN ANY WAY WHILE DOING YOUR HOMEWORK, even if you acknowledge that.


Working from home

All the software you need to work from home is available for free. See resources below and class notes for links (the links on this page will be periodically updated).


Resources