User:Boris/Temp/APB

Timetable and syllabus

Interaction databases

Cytoscape

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 Enrichment analysis Principles of Statistics in molecular biology R, and Bioconductor Clustering and partitioning 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	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