User:Boris/Temp/APB

Timetable and syllabus

I n t r o d u c t i o n
Week	Date	Contents	Activities	Assignment
1	Jan. 9 - 14	Introduction to Computational Systems Biology Course Organisation	—	Assignment 1
F u n c t i o n a l   A n n o t a t i o n
Week	Date	Contents	Activities	Assignment
2	Jan. 16 - 21	CSB on the Web: Databases and services GO, OMIM and other phenotype databases Data mining Data integration: Loose coupling, combining datasets to improve annotation quality, evidence combination Prediction of function	Quiz 1	Assignment 2
"-omics"
Week	Date	Contents	Activities	Assignment
3	Jan. 23 - 28	Working with -ome scale data R and Bioconductor Clustering and partitioning Enrichment analysis Informal programming with perl/php/MySQL/ IDE - Komodo, KDevelop (also Eclipse, except no Perl)	Quiz 2, project concept due	Assignment 3
4	Jan. 30 - Feb. 3	Genomics The transcriptome	Quiz 3	Assignment 4
5	Feb. 6 - 10	Proteome Interactome Metabolome Glycome Lipidome	Quiz 4, project outline due	Assignment 5
I n t e r a c t i o n s ,   P a t h w a y s   a n d   N e t w o r k s
Week	Date	Contents	Activities	Assignment
6	Feb. 13 - 17	Cytoscape Graph theory, graph types and metrics; small-world or random-geometric, date-hubs and party-hubs	Quiz 5	Assignment 6
	Feb. 20 - 24	Reading Week - School closed
7	Feb. 27 - Mar. 2	The biology of protein-protein interactions; physical vs. genetic interactions Interaction databases Interaction prediction, Interologs	Quiz 6	Assignment 7
S y s t e m s
Week	Date	Contents	Activities	Assignment
8	Mar. 5 - 9	Gene regulatory networks Signal transduction networks Metabolic networks KEGG, BioCYC	Quiz 7	Assignment 8
9	Mar. 12 - 16	Extracting regulatory networks from gene expression data Extracting systems from -omics datasets through mutual information	Quiz 8	Assignment 9
10	Mar. 19 - 23	Structural network analysis http://www.csb.ethz.ch/research/structural Systems dynamics http://www.csb.ethz.ch/research/dynamic	Quiz 9, project final submission due	Assignment 10
M o d e l s
Week	Date	Contents	Activities	Assignment
11	Mar. 26 - 30	Modelling methods: ODEs, PDEs and their stochastic counterparts Petri Nets Cellular Automata) process calculi (pi-calculus, ) Model representations (SBML, CellML) Modelling examples(E-Cell, M-Cell, Virtual Cell)	—	Assignment 11
12	Apr. 2 - 6	Constraint based modelling, Flux balance analysis Computational Synthetic Biology http://www.csb.ethz.ch/research/synthetic	—	Assignment 12