Biology Oriented Curriculum in Bioinformatics

1
Biology Oriented Curriculum in Bioinformatics

• Ricardo González Méndez, PhD
• University of Puerto Rico School of Medicine
• Summer Bioinformatics Institute PSC 2008

2
Bioinformatics Curriculum Subject Matter
Components

• Bioinformatics
• Sequence Analysis
• Structural Bioinformatics
• Systems Biology
• Biology
• Introductory Biology/Biochemistry for Computer
  Science and Mathematicians
• Basic Mathematics for Bioinformatics
• Basic Computer Science for Biologists

3
Key Course Developments

• Learning Objectives
• Course Outlines
• Course Syllabi
• Lecture Notes and Slides
• Instructor Guides
• Biology Relevant Problem Sets
• Problems should be based in biologically relevant
  data
• Methodology as taught and practiced must be
  useful to a Biologist
• Evaluation and Outcome Assessment Tools

4
Bioinformatics Components

• Sequence Analysis - Phylogenomics
• Sequence Analysis
• Molecular Phylogenetics
• Basic Structure Modeling
• Visualization of Alignments, Trees and Structure
  Models

5
Bioinformatics Components

• Structural Bioinformatics
• Deriving and visualizing macromolecular
  structures
• Examining and interpreting structural data
• Modeling Protein Structure

6
Bioinformatics Components

• Systems Biology
• Gene Expression
• Microarrays
• Data Analysis
• Proteomics
• Protein Expression
• Protein Interactions
• Analysis and Prediction of Metabolic Networks
• Cellular Modeling

7
Introduction to Bioinformatics I - Applied
Phylogenomic Analysis

• UPR - School of Medicine course taught under
  Dept. of Biochemistry since 2002
• Typically 3-6 students with an additional 2-3
  auditing (students,post-docs or junior faculty)
• 4 master students and 18 PhD students
• Over 60 have a Bioinformatics component in their
  research, thesis or dissertation
• Upon graduation 2 students have obtained post-doc
  positions with substantial bioinformatics
  component and 1 student started a PhD program
  with a major component in bioinformatics
• Several publications being written derived from
  course-work

8
Introduction to Bioinformatics I - Applied
Sequence Analysis

• Required work
• Homework problems
• Course Project
• Project Presentation
• Paper
• Practical Exercises
• Similar to those used in PSC Summer workshop

9
Phylogenomics Course Outline

• Intro to Computer Systems and Unix
• Intro to Databases and Biological Databases
• Basics of Sequence Retrieval and Pairwise
  Alignments
• Fundamentals of Multiple Sequence Alignments
• Patterns and Motifs
• Basic Structure Modeling
• Basic Molecular Evolution of Proteins
• Analysis of Protein Families
• Visualization of Alignments and Structure Models

10
Applied Structural Bioinformatics

• Current State of Development
• One semester or quarter - 3 unit graduate course
• Outline available
• Syllabus available
• Slides - under development - target deadline late
  2008
• Structural Biology exercises - under development
  - target deadline late 2008
• Instructors Guide - future development
• Evaluation and Outcome Assessment - future
  development - target deadline late /2009

11
Structural Bioinformatics Outline

• Objectives
• Introduce students to the biological databases
  available for the analysis of biological
  structures and protein structures.
• Characterize new structures using various
  structural classification library databases and
  algorithms.
• Understand the fundamental biological, chemical
  and physical principles that determine protein
  structure.
• Use structural patterns and folds to determine,
  predict and refine the structure of proteins and
  other biomolecules.
• Use structural information to further establish
  the phylogenetic relationship, if any, between
  protein sequences.
• Use the results of a sequence analysis project
  for structural modeling.

12
Course Outline - Part 1

• Deriving and visualizing macromolecular
  structures
• Review of Protein Structure fundamentals
• X-ray Structures
• NMR Structures
• Electron microscopy
• Structure visualization
• Review of sequence analysis basics - Database
  searches, Classification libraries, multiple
  sequence alignments, and sequence motif detection

13
Course Outline - Part 2

• Examining and interpreting structural data
• Protein Data bank (PDB)
• Structure classification databases (CATH, SCOP)
• Structure validation software
• Secondary structure assignment and prediction
• Structure comparison and alignment
• Domain assignment

14
Course Outline - Part 3

• Modeling Protein Structure
• Comparative Assessment of protein Structure
  Prediction (CASP)
• Comparative modeling
• Fold recognition
• Abinitio structure prediction
• Molecular Mechanics and Dynamics for modeling
  function and mechanisms
• Structural Proteomics

15
Applied Structural Bioinformatics

• Required work
• Homework problems
• Course Project
• Project Presentation
• Paper
• Practical Exercises
• Searching Structural Databases
• Visualizing Protein Structures
• Basic sequence analysis
• Secondary Structure Prediction
• Modeling Protein Structure - Modeller and Rosetta

16
Biology for Computer Scientists and
Mathematicians

• Course to be developed for CS and Math Curriculum
  Track - future development - target 2008-2009
• Intro to Biology and Biological Systems
• Cellular Systems and Structure
• Basic Molecular Biology
• Gene and Genome Structure
• Proteins Structure and Function
• Evolution of Organisms, Molecules, and Systems
• Basic Population Biology and Genetics
• Biological and Medical Imaging
• Molecular Basis of Disease