Week 1
Class 1: Overview
of the course
Course description, intended audience, goals of the course, specific
objectives, course format, grading policy, general approach,
introduction to biological topics. The structural organization of the
body as an intellectual framework for understanding normal and abnormal
biological function. Bioinformatics as the informatics of all basic
biomedical sciences. Structural informatics as a methodology for
representing and organizing information in terms of the structure of
the body.
Week 2
Class 1: Organs and macroscopic anatomy
Physical structure of the body at the visible level, from the whole
body to organ parts and components. Anatomic conventions, regional
(e.g., thorax, head) and systemic (e.g., respiratory system)
approaches, primary classes of anatomical structures (eg., organ, body
part), macroscopic anatomy of the lung as a specific example.
Class 2: Anatomical Knowledge Representation
Representing non-image-based (symbolic) knowledge about the structure
of the body. Use of such knowledge as a means for organizing and
relating other information. The Foundational Model of Anatomy and other ontologies.
Week 3
Class 1: Tissues and cells
Physical structure of the body at the microscopic and cell
ultrastructural level. Tissues and tissue types (e.g., epithelium,
connective tissue), cells and cell types (e.g., muscle cell, nerve
cell), cell components (e.g., nucleus, plasma membrane). Lung tissue
and cell types.
Class 2: Imaging informatics
Images as a major source of information about the structure and
function of the body. Types of images, overview of image processing,
image databases, visualization, relating images to symbolic
descriptions of anatomy.
Week 4
Class 1: Macroscopic Physiology
Physiology as the study of the transformation of anatomical structures
over short periods of time. Systems physiology at the macro level
(e.g., the cardiac or respiratory cycle).
Class 2: Simulation
Systems for simulating physiological function, The Virtual Human.
Simulating the heart. Jsim and other modelling systems. Ontology-based
model integration.
Week 5
Class 1: Molecules and Pathways
Biochemical foundations: atoms, molecules, covalent and other bonds,
chemical energetics, the role of enzymes, metabolic pathways in the
cell, glycolysis as an example pathway.
Class 2: Pathway databases
Pathway databases such as Ecocyc.
Week 6
Class 1: Proteins
Structure and function of proteins
Class 2: Protein structure determination, protein
databases
Methods for determining, analyzing and visualizing protein structure;
protein databases.
Week 7
Class 1: DNA and protein synthesis
The structure of nucleic acids, the fundamental dogma of biology.
Class 2: Sequencing and databases
Methods for sequencing DNA, analyzing and comparing sequences, sequence
databases, links to protein databases.
Week 8
Class 1: Gene regulation
The control of protein synthesis, glycolysis as an example
Class 2: Measuring and managing gene expression data
Microarrays, in situ methods, analysis approaches, databases
Week 9
Class 1: Developmental biology
Class 2: Developmental biology Informatics
Week 10
Class 1: Pathology and Cancer
Class 2: Cancer informatics
Week 11
Class 1: Cell signalling
Control of gene expression through contact with other cells, glycolysis
as an example
Class 2: Systems biology
Simulating the functioning cell.
Week 12 Finals week