Transcript Introductory course in Bioinformatics

Introductory course in
Bioinformatics
1st year freshman from any discipline
of Science & Engineering
3 Credit hours course
12 weeks module
Pre-requisites
• Concept of Basic Algebra.
• Knowledge of writing mathematical expression from
word problems and from simple physical aspects.
• Knowledge of Basic Descriptive Statistics, such as
Central Tendency of frequency (data), Probability,
Histogram etc.
• Basic concept of using computer, such as managing
data files, word files, text files etc.
• Concepts of DNA, mRNA, nucleic acid. Amino acid etc.
• Concepts of Gene.
• A little bit of knowledge of the biological system in which
the student is interested (can be developed with his own
during the course).
Learning Outcomes
At the end of this course, students will be able to:
- Use freely available bioinformatics tools.
- Form a biological hypothesis to guide data analysis
and interpretation.
- Collect an appropriate data set for evaluating
their hypothesis.
- Provide a basic outline of the process used for
global and local alignment.
Lesson plan for Week-1
• An overview of the field of Bioinformatics – its
importance, roles to unfold the mysteries of
complex biological systems.
• Introduction of different text books and reference
books in bioinformatics.
• Reviews on computer skills via small biological
systems such as population growth, preypredator relationship using Excel spreadsheet.
(Ref: BioQuest Curriculum Consortium, Jungck,
Fass and Stanley)
Lesson plan for week-2
• Information of protein structures.
• Basic knowledge of protein and amino acid
chemistry.
• Introduction of PAM : Point Accepted Mutations.
Hands on experience on development of
Dayhoff’s matrix in order to understand welltolerated, conserved, single amino acid changes
in highly conserved sequences.
(Mathematical frame work of Dayhoff’s matrix and
its optimization involves dynamic optimization
hence out of the scope of this level)
Lesson plan for week-3
• Introduction to MATLAB.
• Develop program writing skill for small biological
problems that involves both continuous and
discrete variables with and without delays.
• Introduction to Statistics toolbox, Bioinformatics
toolbox and Simbiology toolbox in MATLAB.
(It helps students to build their own code for
different algorithms – it also bypass the knowledge
of calculus if the students are not very much
familiar with calculus)
Lesson plan for week-4
Task: Explain scoring function to provide insight to how sequences are aligned
Focus: Needleman-Wunsch Algorithm; global alignment of two sequences
Needleman, SB and Wunsch, CD. A general method applicable to the search for
similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453, 1970.
Key Concept: The best alignment mathematically speaking is NOT ALWAYS
the best alignment biologically. We must balance our interpretation of an alignment
using our knowledge of biology.
Activity: Students perform global alignments using ALIGN at Biology Workbench,
a global alignment using a dynamic programming strategy developed by Myers & Miller.
Students make graphs in Excel to investigate how alignment score is changed by
altering gap open, gap extension, and other parameters.
Lesson plan for week-5
Task: Introduce students to Hands-On HIV session at BioQUEST
Focus: Working with sequence data; forming a biologically meaningful hypothesis;
Key Concept: A biologically meaningful hypothesis gives focus and purpose to
bioinformatics analysis.
Activity: Students work on BioQUEST HIV exercise.
http://bioquest.org/bedrock/problem_spaces/hiv/index.php
Lesson plan for week-6
Task: Students choose an independent project for remainder of semester
Focus: Provide examples of possible projects and outline project flow
Key Concept: Students will feel ownership of a project they choose and design (within
provided guidelines). Students will have opportunity to apply bioinformatics tools to
gain information on a system using real data.
Activity: Students explore possible projects.
CFTR: http://bioquest.org/bioinformatics/module/tutorials/Cystic_Fibrosis/index.html
HIV: http://bioquest.org/bedrock/problem_spaces/hiv/index.php
OMIM: http://www.ncbi.nlm.nih.gov/Omim/omimhelp.html#SampleSearches
MHC: http://www.ncbi.nlm.nih.gov/gv/mhc/main.cgi?cmd=init (dbMHC at NCBI)
http://www.ncbi.nlm.nih.gov/gv/mhc/html/tutorial.html
Influenza Virus: http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
Lesson plan for weeks-7-12
Students continue work on their independent project.
Student progress is reviewed/supported by weekly meeting with professor,
and by peer-sharing of progress.
Students are encouraged to provide advice and suggestions to one another.
Lesson plan for weeks-13-14
Group presentation of completed projects.
Sharing in a public forum would be advantageous.
This is a work in progress,
and we welcome suggestions and comments!