MATH 6685/CCOM 4995 - Computer Applications in Biology - Spring 2020

University of Puerto Rico
Rio Piedras Campus
College of Natural Sciences
Department of Computer Science

Professor

Field Value
Name Humberto Ortiz-Zuazaga
Office NCL A-159
Laboratory NCL A-158
Telephone 787-764-0000 x88363
email humberto.ortiz@upr.edu
Web page https://ccom.uprrp.edu/~humberto/
Office hours Monday, Wednesday 10:00 AM - 12:00 PM
or by appointment

Credits

3 credits

Description

Introductory graduate/undergraduate course in bioinformatics. Topics covered will include biological sequences, programming in python, UNIX, sequence alignments, sequence phylogeny, sequence database searches, and gene expresion analysis, including microarray and RNA-Seq analysis, and gene set or pathway analysis.

We will emphasize the fundamental theory behind the analysis, and also present practical problems and their solutions. The course will use open-source bioinformatics tools such as bioconductor, and show how to construct such tools using python, R, or other languages.

Prerequisites

MATE 3026 or MATE 3028 or CCOM 3033

The course is designed for graduate and advanced undergraduate students in biology or computer science. Students should have some familiarity with programming.

Course schedule

The course will meet Thursdays and Fridays from 11:30AM-12:50PM in room CNL A-143, Natural Sciences, Rio Piedras Campus, University of Puerto Rico.

Objectives

Introduce students to fundamental concepts in bioinformatics, programming, algorithm design and analysis. After completing the course, students should be able to select tools and programs to solve bioinformatic problems and participate in their development.

Calendar

The proposed schedule of lectures, subject to change:

Date Topic Reading
Jan 30 Introduction: History of Bioinformatics Chapter 1, 2
Jan 31 Ethical Issues in Bioinformatics web page
Feb 6-7 Sequences: Nucleic Acids and Proteins Chapter 3
Feb 13-14 Computer platforms used in sequence analysis
Feb 20-21 Brute force - Restriction mapping Chapter 4
Feb 27-28 Greedy algorithms - Gene order Chapter 5
Mar 5,6,12 Dynamic Programming - Pairwise Sequence Alignment Chapter 6
Mar 13 First Partial Exam
Mar 19,20,26 Graph Algorithms - Sequence Assembly Chapter 8
Apr 2-3 Combinatorial Pattern Matching - Fasta and BLAST Chapter 9
Apr 16-17 Clustering and Trees- Phylogeny Chapter 10
Apr 5 Functional Genomics: Microarrays
Apr 23-24 Statistical Methods for Analysis of Gene Expression
Apr 30, May 1 Gene Regulatory Networks: Reverse Engineering
May 7-15 Final Projects

Alternative Teaching Methods

Certification No. 112 (2014-2015) of the Governing Board defines a classroom course as a course in which 75% or more of the hours of instruction require the physical presence of the students and the teacher in the classroom. This means that 25% of a classroom course could be offered without requiring the physical presence of the students and the teacher in the classroom. If necessary, this course will be able to complete up to 25% of the contact hours (11.25 hours) on a non-face-to-face basis by alternative methods such as: videoconferences, instructional modules, discussion forums and others. If so, the calendar/agenda will be modified to include the topics that will be covered by alternative methods.

Instructional strategies

The professor will discuss each topic, students will complete a practical excercise for each bioinformatic technique discussed in class.

Instructional resources

The course will be hosted on the UPRRP Moodle. Register and stay tuned for our polls and forum postings.

Textbook:

An Introduction to Bioinformatics Algorithms. Neil C. Jones and Pavel A. Pevzner. ISBN-10: 0-262-10106-8 ISBN-13: 978-0-262-10106-6

Evaluation

Students work will be evaluated on a 100% basis with the standard curve.

  • Participation in course forums (online, classroom), 25% final grade
  • Homework, 25% final grade
  • Partial exam, 25% final grade
  • Final presentation, 25% final grade

REGULATION ON DISCRIMINATION BY SEX AND GENDER IN THE FORM OF SEXUAL VIOLENCE

The University of Puerto Rico prohibits discrimination based on sex, sexual orientation, and gender identity in any of its forms, including that of sexual harassment. According to the Institutional Policy Against Sexual Harassment at the University of Puerto Rico, Certification Num. 130, 2014-2015 from the Board of Governors, any student subjected to acts constituting sexual harassment, must tum to the Office of the Student Ombudsperson, the Office of the Dean of Students, and/or the Coordinator of the Office of Compliance with Title IX for an orientation and/or a formal complaint.

REASONABLE ACCOMMODATION

The University of Puerto Rico complies with all state and federal laws and regulations related to discrimination, including “The American Disabilities Act” (ADA law) and Law #51 from the Puerto Rico Commonwealth (Estado Libre Asociado de Puerto Rico). Every student has the right to request and receive reasonable accommodation and Vocational Rehabilitation Services (VRS). Those students with special needs that require some type of particular assistance or accommodation shall explicitly communicate it directly to the professor. Students who are receiving VRS services shall communicate it to the professor at the beginning of the semester so that appropriate planning and the necessary equipment may be requested according to the Disabilities Persons Affairs Office (Oficina de Servicios a Estudiantes con Impedimentos –OSEI) from the Students’ Deanship office. Any other student requiring assistance or special accommodation shall also communicate directly with the professor. Reasonable accommodations requests or services DO NOT exempt the student from complying and fulfilling academic and course related requirements and responsibilities.

ACADEMIC INTEGRITY

The University of Puerto Rico promotes the highest standards of academic and scientific integrity. Article 6.2 of the UPR Students General Bylaws (Board of Trustees Certification 13, 2009-2010) states that academic dishonesty includes, but is not limited to: fraudulent actions; obtaining grades or academic degrees by false or fraudulent simulations; copying the whole or part of the academic work of another person; plagiarizing totally or partially the work of another person; copying all or part of another person answers to the questions of an oral or written exam by taking or getting someone else to take the exam on his/her behalf; as well as enabling and facilitating another person to perform the aforementioned behavior. Any of these behaviors will be subject to disciplinary action in accordance with the disciplinary procedure laid down in the UPR Students General Bylaws.

To ensure user data integrity and security, hybrid and distance education courses are offered through the institutional learning management system, which employs secure connection and authentication protocols. The system authenticates the users’ identity with the username and password of their institutional accounts. Users are responsible for keeping their password secure and not sharing with others.

References

  1. Neil C. Jones and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms. The MIT Press, Cambridge, Massachusetts, 2004. ISBN-10: 0-262-10106-8 ISBN-13: 978-0-262-10106-6.

  2. Introduction to Computational Biology: Maps, sequences and genomes. Michael S. Waterman. Chapman & Hall/CRC. 1995.

  3. Bioinformatics: Seqence and Genome Analysis, Second Edition. David W. Mount. Cold Spring Harbor Laboratory Press, 2004.

  4. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Dan Gusfield, Cambridge University Press, 1997.

  5. Bioinformatics for Biologists. Pavel A. Pevzner and Ron Shamir. Cambridge University Press, 2011.

  6. H. Ortiz-Zuazaga, Bioinformatics: Principles and Applications, http://www.hpcf.upr.edu/~humberto/presentations/bioinfo-pucpr.html

  7. H. Ortiz-Zuazaga, Notas de la clase, presentaciones, 2009, http://moodle.hpcf.upr.edu/course/view.php?id=10