HOME	MEBI 534 , Autumn 2006 Biology and Informatics
	Class Notes and Assignments  Unless otherwise specified, all assignments should be completed PRIOR to the class with which they are associated. Class Project: due at the end of the day on December 8. Class Presentations: one per student during the quarter Midterm Exam: due  Oct 27 Week 1 Class 1 Introduction  Slides Week 2 Class 1 Organs Assignment Slides Class 2 Knowledge Representation in Anatomy Assignment Week 3 Class 1 Tissues and Cells Assignment Slides Class 2 Imaging Informatics Assignment       Week 4 Class 1 Macroscopic Physiology Reading assignments:  Seifter2005 Chapter 16 Seifter2005 Chapter 17           Cook slides Class 2 Simulation Reading Assignments: Read Hunter 2003, "Integration from Proteins to Organs: the Physiome Project". Be familiar with the Physiome web site. Check out the cardiopulmonary mechanics model from this site (assembled by Max Neal).  Read Cook 2004, "The Foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions"   Be prepared to discuss the meaning of a simulation model.           Cook slides Week 5 Class 1 Proteins Reading: AlbertsECB Chapter 4 Class 2 Protein structure and databases Reading Assignments:  Berman 2000, The Protein Data Bank Beck2000, Molecular Dynamics           Dagget slides Week 6 Class 1 Molecules and pathways Reading: AlbertsECB Chapter 2, AlbertsECB Chapter 13 Slides Glucose molecule movie Palmitic acid molecule movie ATP molecule movie Citric acid cycle movie Class 2 Pathway databases and simulation Reading Assignments:  Cortassa 2003 - includes a mathematical model of the Krebs Cycle. No need to read this carefully, but be able to explain how this type of model relates to the modeling described by Karp Karp 2001, Pathway databases: a case study in computational symbolic theories Schaefer 2004, Pathway databases (review)   Week 7 Class 1 DNA and protein synthesis Reading: Alberts ECB Ch 7 Myler slides: DNA and the Central Dogma Myler slides: Genome sequencing Class 2 Sequencing and sequence databases Reading Assignments:   GenBank BLAST Gene Ontology Myler slides: Sequence analysis Gene Ontology Sequence databases Week 8 Class 1 Gene regulation Reading: Alberts ECB Ch 8     Class 2 Gene expression and databases Reading Assignments:  Stoeckert2002  Array databases and standards  Quackenbush2001  Array analysis Christiansen 2006 EMAGE gene expression atlas Week 9 Class 1 Immunology Reading:  Janeway 5th edition, Chapter 1 Stevens 2005 Stevens slides Class 2 Immunology informatics Reading:  Jakobovits 2002  - local lab management systems DeGroot 2006 - immunomics Optional: Christie Fong 2006 - CELO, basis for Stevens system Hao Li 2006 - model driven local lab management systems Brusic 2002 - Epitope mapping methods referred to in DeGroot Immunome Research (check out top 10 articles) Week 10 Class 1 Cell signalling Reading: Alberts ECB Ch 16 Xu slides Class 2 Systems biology and data integration Reading: Ideker2001 Systems Biology Louie 2006 Data integration systems Optional: Ishii 2004  Cell modelling Strange 2005 Relationship between systems biology and physiology Hucka2004  Systems Biology markup language Biomediator 2004 Week 11 Class 1 Pathology, with emphasis on  cancer Reading:  Cancer, Chapter 23 in Alberts 4th edition Slides Class 2 Pathology and cancer informatics Reading:  Sinard 2001 Pathology informatics Salz 2006 CaGrid, a component of caBig Optional: Explore the caBIG web site
BACK TO TOP  Last Updated: 11/20/06	Contact the instructor at: brinkley@u.washington.edu