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
D a t a
Week	Date	Contents	Activities	Assignment
2	Jan. 16 - 21	Databases and tools CSB on the Web: Databases and services Data integration GO, OMIM and other phenotype databases Prediction of function	Quiz 1	Assignment 2
3	Jan. 23 - 28	Working with -ome scale data: the concept of Gene lists Enrichment analysis and GSEA Principles of Statistics in molecular biology and Exploratory Data Analysis R, and Bioconductor Clustering and Classification Data mining Informal programming with perl/php/MySQL/ Integrated Development Environments	Quiz 2, project concept due	Assignment 3
"-omics"
Week	Date	Contents	Activities	Assignment
4	Jan. 30 - Feb. 3	Genome 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	Interaction Networks; Interaction biology, principles, physical vs. genetic interactions Interaction databases Cytoscape	Quiz 5	Assignment 6
	Feb. 20 - 24	Reading Week - School closed
7	Feb. 27 - Mar. 2	Graph theory, graph types and metrics; small-world or random-geometric, date-hubs and party-hubs 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; Also: Extracting regulatory networks from gene expression data Signal transduction networks Metabolic networks KEGG, BioCYC	Quiz 7	Assignment 8
9	Mar. 12 - 16	Extracting systems from -omics datasets through mutual information	Quiz 8	Assignment 9
10	Mar. 19 - 23	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 principles: Modelling methods: ODEs, PDEs and their stochastic counterparts Constraint based modelling Flux balance analysis 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	Computational Synthetic Biology http://www.csb.ethz.ch/research/synthetic	—	Assignment 12