Fall 2017 - MBB 200 D100

Selected Topics in Molecular Biology and Biochemistry (3)

Special Topics Data Analysis for MBB

Class Number: 4752

Delivery Method: In Person

Overview

  • Course Times + Location:

    We, Fr 2:30 PM – 4:20 PM
    AQ 5016, Burnaby

  • Exam Times + Location:

    Dec 13, 2017
    3:30 PM – 6:30 PM
    AQ 5037, Burnaby

  • Prerequisites:

    Will be announced before the start of the term and will depend upon the nature of the topic offered.

Description

CALENDAR DESCRIPTION:

The topics in this course will vary from term to term, depending on faculty availability and student interest.

COURSE DETAILS:

Selected Topic: Data Analysis for Molecular Biology

The purpose of this introductory data analysis course is to teach students in molecular biology or any students who will analyze molecular data, basic knowledge of molecular biology data types, data analysis methods including basic programming skills using Python, and basic statistics skills using R.

Lectures

Lecture 1 Molecular biology data and data analysis.
Lecture 2 Molecular sequences: features & composition.
Lecture 3 Gene splicing and GFF data format.
Lecture 4 Sequencing analysis using Biopython.
Lecture 5 Quantitative DNA analysis using Python conditional test.
Lecture 6 Searching for restriction sites in DNA sequences.
(Midterm exam)
Lecture 7 Searching for sequence features in protein sequences.
Lecture 8 Genetic code and DNA translation.
Lecture 9 Quantitative analysis of genes using R.
Lecture 10 Analyzing genomics big data using R data frame.
Lecture 11 Genome annotation using R data frame and R graphics.
Lecture 12 Genome analysis using Bioconductor.
(Final exam)

Labs

Lab 1Learning Python: printing and manipulating sequences.
Lab 2Reading and writing sequence files.
Lab 3Lists, loops, reading large sequence files.
Lab 4Writing our own functions for processing sequences.
Lab 5Quantitative DNA analysis using Python conditional test.
Lab 6Using regular expressions to search for sequence features in DNA sequences.
Lab 7Using regular expressions to search for sequence features in protein sequences.
Lab 8Translating DNA sequences using Python dictionaries.
Lab 9Learning R: molecular data analysis and presentation.
Lab 10Working with genome-scale sequences.
Lab 11Using R data frames and R graphics
Lab 12Technical review

Grading

  • In class lab tasks: In each lab, there is a list of tasks that should be accomplished in class. Results are submitted by the end of each lab. 20%
  • Lab assignments: Short assignments will be handed out in lab sessions and will be due at the start of your lab one week later, unless indicated otherwise. There is a 10% per day late penalty for assignments received after the due date time. 35%
  • Midterm and Final exams - a mixture of multiple choice, short answer and written questions. (10% for midterm exam and 30% for final exam) 35%
  • Participation (iClicker pre-lecture quiz) 10%

NOTES:

Students with credit for CMPT 102, 120, 125, 126, 128 or 130 may not take this course for further credit.

REQUIREMENTS:

Prerequisites: MBB222 and MATH152 or MATH155

Materials

REQUIRED READING:

Python for Biologists.  Martin Jones.  2013. CreateSpace Independent Publishing Platform.
ISBN: 978-1492346135

Department Undergraduate Notes:

  • Students are advised to review the plagiarism tutorial found at
    http://www.lib.sfu.ca/help/tutorials/plagiarism-tutorial
  • For help with writing, learning and study strategies please contact the Student Learning Commons at
    http://learningcommons.sfu.ca/
  • Students requiring accommodations as a result of a disability, must contact the Centre for Students with Disabilities (778-782-3112 or e-mail:  csdo@sfu.ca)

Registrar Notes:

SFU’s Academic Integrity web site http://students.sfu.ca/academicintegrity.html is filled with information on what is meant by academic dishonesty, where you can find resources to help with your studies and the consequences of cheating.  Check out the site for more information and videos that help explain the issues in plain English.

Each student is responsible for his or her conduct as it affects the University community.  Academic dishonesty, in whatever form, is ultimately destructive of the values of the University. Furthermore, it is unfair and discouraging to the majority of students who pursue their studies honestly. Scholarly integrity is required of all members of the University. http://www.sfu.ca/policies/gazette/student/s10-01.html

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS