CS612: Algorithms in Bioinformatics

 Fall 2017

Mo We 5:30-6:45, M-2-207

 

Instructor

Course Description

Textbook

Evaluation

Homework and Term Projects

Coursework (Links and PDF slides are posted here)

Resources

Accommodations

Student Conduct


Instructor  

Nurit Haspel
Office: S-3-071
Office Hours: Monday, Wednesday 2:30-4:00pm or by appointment
Office Phone: 617-287-6414
e-mail: nurit.haspel@umb.edu
Homepage: http://www.cs.umb.edu/~nurith


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 are CS210 (Intermediate Computing) and MATH 260 (Linear Algebra) or permission from the instructor.


Recommended Textbooks

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

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


Grade Evaluation

Homework assignments: 40-50% (4-5 homework assignments will be given)
Project and Final Presentation: 50-60%

Homework assignments

<
Assignment (PDF) Posted/Given on Due Date Handouts Sample Solution
HW1 Sep. 25, 2017 Oct. 11, 2017 BLAST how-to solution
HW2 Oct. 11, 2017 Oct. 18, 2017 VMD
UCSF Chimera
solution
HW3 Oct. 25, 2017 Nov. 8, 2017 set1.txt
set2.txt
Protein Investigator page
solution
hw3.R hw3.m
HW4 Nov. 20, 2017 Dec. 4, 2017 hw4.R
HW5 Dec. 4 2017 Dec. 11 2017

 


Syllabus

Week

Topic

Book Chapters

Session Dates

Session Info

Slides/notes

1

Introduction,
basic concepts

--

Wednesday,
September 6

Introduction

Introduction

2

Finish up intro
Sequence Alignment

Lesk: Chapter 4

Monday,
September 11

Finish up introduction,
sequence comparison

Wednesday,
September 13

Sequence alignment, BLAST

Sequences

CS310 DP class notes

3

Sequence alignment
MSA
Protein structure

Lesk, Ch. 5

Monday,
September 18

Sequence Alignment
BLAST

Lesk, Ch. 6
Bourne & Gu, Ch. 2

Wednesday,
September 20

Multiple Sequence Alignment
Start Structure

4

MSA
Protein Structure

Lesk, Ch. 6
Bourne & Gu, Ch. 2

Monday,
September 25

Protein Structure basics
Secondary, tertiary structures

Protein structure

Wednesday,
September 27

5

Structure
Visualization

Lesk: Ch. 4
Bourne & Gu, Sec. 2 (Ch. 10-13)

Monday,
October 2

Structure

Wednesday,
October 4

Databases

Databases

6

Protein Structure
Visualization, databases

Lesk: Ch. 4
Bourne & Gu, Sec. 2 (Ch. 10-13)

Monday
October 9

No class
(Columbus day)

Same (slightly revised)

Wednesday,
October 11

Databases
Visualization

Same (slightly revised)

Visualization

7

Visualization
Protein Folding

Bourne & Gu: Ch. 30

Monday,
October 16

Homology modeling

Notes- Folding

Bourne & Gu: Ch. 31

Wednesday,
October 18

Folding Algorithms

8

Folding
Quality Assessment

Monday,
October 23

Folding

Folding (revised)

Wednesday,
October 25

9

Folding methods
quality assessment

Monday,
October 30

Folding Methods

Notes - Folding Methods

Wednesday,
November 1

10

Folding
Bio Simulations

Monday,
November 6

Homology modeling
Distance Measurement

Notes - Quality Assessment

Wednesday,
November 8

Start biosimulations

Biomolecular Simulations

11

Simulations
Geometric Manipulation

Monday,
November 13

Simulations

Bourne & Gu: Ch. 16

Wednesday,
November 15

Notes - Manipulation

12

Manipulation
Struct. Alignment

Monday,
November 20

Same (revised)

Wednesday,
November 22

13

Structural Alignment
Docking

Monday,
November 27

Structural alignment

Notes - Structural Alignment

Wednesday,
April 28

Start docking

Notes - Docking

14

Docking
Robotics Based Sampling

Monday,
May 3

Docking

See last week

Wednesday,
May 5

Flexible Docking
Configuration space?

Notes - Sampling

 


Resources


Accommodations:  Section 504 of the Americans with Disabilities Act of 1990 offers guidelines for curriculum modifications and adaptations for students with documented disabilities. If applicable, students may obtain adaptation recommendations from the Ross Center for Disability Services, Campus Center, UL Room 211, (617-287-7430). The student must present these recommendations and discuss them with each professor within a reasonable period, preferably by the end of Drop/Add period.


Student Conduct:  Students are required to adhere to the University Policy on Academic Standards and Cheating, to the University Statement on Plagiarism and the Documentation of Written Work, and to the Code of Student Conduct as delineated in the catalog of Undergraduate Programs. The Code is available online at: http://www.umb.edu/life_on_campus/policies/code/