HOME	MEDED 534 , Autumn 2005 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 12. Class Presentations: one per student during the quarter Midterm Exam: due  Oct 28 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 Class 2 Imaging Informatics Assignment Slides       Week 4 Class 1 Macroscopic Physiology Reading assignments Review physiology section of Chapter 17 in Anatomy and Physiology,   The Easy Way. Class 2 Simulation Assignment: Read Hunter 2003, "Integration from Proteins to Organs: the Physiome Project". Be familiar with the Physiome web site. Check out the integrative respiratory system models from this site. 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. Week 5 Class 1 Molecules and pathways Reading: Alberts chapter 2 Class 2 Pathway databases Reading Assignment: Schaefer 2004, Pathway databases (review) Karp 2001, Pathway databases: a case study in computational symbolic theories Krieger 2004, MetaCyc Kenehisa 2004, KEGG Week 6 Class 1 Proteins Reading: Alberts chapter 3     Class 2 Protein structure and databases Reading Assignment: Apweiler 2004, Protein sequence databases Berman 2000, The Protein Data Bank Kabsch and Sander 1984, Limitations of 3-D structure prediction methods Moult 2005, Structure prediction competition Week 7 Class 1 DNA and protein synthesis Reading: Alberts chapter 4, pp 191-192 (Intro)                                              pp 192-197 (Structure and Function of DNA)                Alberts chapter 6 Myler Slides Class 2 Sequencing and sequence databases Assignment:    Patnaik 2001Review of online tools and databases for sequence                      analysis   Benson 2004  Genbank sequence database   GO 2004 Gene Ontology   Gennari 2004 Mapping FMA to GO Myler slides Week 8 Class 1 Developmental Biology Reading: Alberts chapter 21 Roelink slides Class 2 Informatics in Developmental Biology Assignment: Davidson2001: Beyond Sequence Badock2003: EMAP and EMAGE Burger2004: Formalization of mouse embryo anatomy Ideker2001: Systems Biology Week 9 Class 1 Gene regulation Reading: Alberts chapter 7 Wenqing Xu slides     Class 2 Gene expression and databases Assignment:   Freeman2000 Expression arrays   Stoeckert2002  Array databases and standards   Quackenbush2001  Array analysis   Suzuki 2004 In situ hybridization   Pandey2000 Proteomics Week 10 Class 1 Cell signalling Reading: Alberts chapter 15 Wenqing Xu slides Class 2 Systems biology  Assignment:    Lee2003     Quantitative pathway modelling   Cook2001   Qualitative pathway modelling   Hucka2004  Systems Biology markup language   Luciano2005 BioPAX   Neuman2005 Life Sciences Semantic Web Week 11 Class 1 The neuron and neuroscience Reading: Lodish 4th Edition, Chapter 21 Ric Robinson slides Class 2 Neuroinformatics Assignment: Miller2001 SenseLab neuron and modelling public database Bales2005 XML-based data integration Mazziotta2001 Probabilistic brain atlases Hines2002 NEURON computional modeling software
BACK TO TOP  Last Updated: 9/8/05	Contact the instructor at: brinkley@u.washington.edu