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 representation
schemes.
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 Soldier initiative.
Simulating the heart. Jsim and other modelling systems.
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:Cell signalling
Control of gene expression through contact with other cells, glycolysis
as an example
Class 2: Systems biology
Simulating the functioning cell, simulating control of the glycolytic
pathway
Week 10
Class 1: From molecules to organs
Protein complexes, intracellular structural components, cell adhesion
molecules, cells to tissues and tissues to organs.
Class 2: 3-D structural modelling
Methods for acquiring structural data, representations and algorithms,
visualization.
Week 11
Class 1: The neuron and neuroscience
The neuron as a specialized cell type. Properties of the neuron, the
action potential, synapses, neural circuits, the macroscopic brain,
behaviour. The field of neuroscience as one of many fields that rely
on the basic principles outlined in this course.
Class 2: Neuroinformatics
Information representation, management and sharing in neuroscience.
The Human Brain Project.
Week 12 Finals week