User:Boris/Temp/APB

Timetable and syllabus

I n t r o d u c t i o n
Week	Date	Topics	Activities	Assignment
1	Jan. 9 - 14	Computational Biology aims to bring biology from its descriptive beginnings to a truly predictive science, based on consistent and well understood principles. In the systems biology field of computational biology, we deal primarily with large-scale, cross-sectional data, its relationships and hierarchies. Course Organisation Introduction to Computational Systems Biology	—	Assignment 1
D a t a
Week	Date	Topics	Activities	Assignment
2	Jan. 16 - 21	In principle, most of the data of interest to us is freely available on the Web, in public repositories. However, the number of databases and associated Web services is large and in constant flux and integrating the data has its own issues. The most important issue is the question of how to define function and make this concept computable; from this arises the central role that ontologies play in the field. CSB on the Web: Databases and services Data integration Ontologies and phenotypes Prediction of function	Quiz 1	Assignment 2
3	Jan. 23 - 28	The large volume of data in any given systems biology experiment basically precludes the manual, gene-by-gene analysis of results. Questions arise regarding computational strategies for gene lists, especially the statistical tools and strategies we have at our disposal, and a minimum set of programming and automation skills. Lists of genes - a common outcome of high-throughput experiments Gene lists Enrichment analysis The GSEA approach Statistics Principles of Statistics in molecular biology R Bioconductor Clustering and Classification Exploratory Data Analysis Data mining Programming Informal programming Using an IDE (Integrated Development Environments)	Quiz 2, project concept due	Assignment 3
"-omics"
Week	Date	Topics	Activities	Assignment
4	Jan. 30 - Feb. 3	Genome sequencing brought the first complete overview of the information underlying life; the associated concept of the transcriptome - a description of which portion of the genome is expressed at what time - is the most basic functional description of this information. Genome Transcriptome	Quiz 3	Assignment 4
5	Feb. 6 - 10	Many more holistic, or cross-sectional descriptions of the molecular composition and assembly of the cell are being worked on. Proteome 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	Theme	Activities	Assignment
6	Feb. 13 - 17	Fundamentally, -omics descriptions provide us with lists of components. However, to understand how things work, we need to address the relationships of the components - how things are put together: the molecular blueprints. At its most basic level, this is the question of molecular interactions in the cell. A quantitative description of molecular interactions relies heavily on the mathematical discipline of graph theory. Cytoscape is a visualization and analysis platform for molecular interactions. Graph theory Cytoscape	Quiz 5	Assignment 6
	Feb. 20 - 24	Reading Week - School closed
7	Feb. 27 - Mar. 2	Here we focus on the biological objects of "Interaction Science". The Interactome Interaction databases Pathways and Networks Interaction prediction	Quiz 6	Assignment 7
S y s t e m s
Week	Date	Topics	Activities	Assignment
8	Mar. 5 - 9	Several key networked systems exist in the cell. Here we discuss their paradigms, how they are constructed from experimental data and examples of how they can be organized in databases. Gene regulatory networks Metabolic networks Signaling networks Developmental networks Pathway and network databases KEGG BioCYC	Quiz 7	Assignment 8
9	Mar. 12 - 16	Information theory has proven to be one of the cornerstones of biological analysis. A good example of its power and utility is the definition of systems in large-scale biological datasets. Extracting systems from -omics datasets through mutual information	Quiz 8	Assignment 9
10	Mar. 19 - 23	Life is not static, only death is. Yet, the dynamic nature of biological systems is often overlooked. Systems dynamics	Quiz 9, project final submission due	Assignment 10
M o d e l s
Week	Date	Theme	Activities	Assignment
11	Mar. 26 - 30	The notion that computational biology will at some time become predictive is tied to the idea that we will be able to model the cell's systems. Many approaches exist, each with its own strengths and weaknesses; how to integrate such models - preferrably across multiple scales - is a question of its own. Modelling principles Model representations Modelling methods Modelling examples	—	Assignment 11
12	Apr. 2 - 6	Do we really understand systems biology? Computational Synthetic Biology is the ultimate test. Computational Synthetic Biology	—	Assignment 12