Data modellering en -verwerking (8C020)

Fall 2007, Semester 1, Block B

Contents:

Announcements:

No lecture on Monday, October 15. Extra lecture hours on Monday, October 22, 7^th and 8^th hour in Auditorium 5.

Time:

Monday, 5^th and 6^th hour (13:30-15:15)

Thursday, 5^th and 6^th hour (13:30-15:15)

Place:

Auditorium

Lecturer:

Dragan Bosnacki
mailto:dragan@win.tue.nl
address: WH 3.101
phone: 040-2475159

Literature:

G.J. Houben, N.H.L. Kuijpers, Collegedictaat Datamodellering en -verwerking (8C020)
A. Silberschatz, H.F. Korth, S. Sudarshan, Database System Concepts (4th Edition), McGraw-Hill, 2002.
Modeling Genetic Networks with Petri Nets
Modeling Genetic Networks with Boolean Functions
Dynamics of Feed Forward Loop Motifs

Term Project:

Links:

Previous Exams and Exercises:

Schedule:

No	Lecture date	Subjects	Remarks
1	October 8	Introduction, Information Systems, Data Bases, Entity-Relationship Model. Slides	Lecture Notes Sections 3.1-3.5 (Sections 2.1-2.6 optional), Book Sections 2.1-2.5
2	October 11	Cardinality, Weak entities, Aspects of the ER-modeling: Multi-valued attributes, repeating group, time-depending data, ISA-relationship, UML; Exercise E-R Modeling: Hospital Example (Solution) . Exercise 3.2 (Student Cleaning Services). Slides	Lecture Notes Sections 3.4, 3.5, 3.6, Book Sections 2.5-2.11
3	October 18	Relational Model, Relational Approach, Tables, Normalization. Translating Entity-Relationship models to Relational Models Hospital Example (RM model). Cleaning Services Example. Slides	Lecture Notes Chapter 4, Book Section 3.1 Extra Story: Codd and Cellular automata, Turing Machine, Von Neumman’s Universal Constructor , Game of Life, Conway about the Game of Life on YouTube.
4/5	October 22 (Two extra hours, 7^th and 8^th)	Normalisation: 1^st, 2^nd, 3^rd normal forms, Query Languages, Data definition and manipulation in SQL, SQL: Joins and Subqueries, Exercises, Normalisation: 1^st, 2^nd, 3^rd normal forms. Slides	Lecture Notes Chapter 5, Book Chapters 3, 7, http://en.wikipedia.org/wiki/Database_normalization
6	October 25	Exercises SQL. Aggregate Functions (max, sum, avg, count, group by, having). Solutions to Exercises Section 5.5. Process Modeling, Transitions Systems, Graphs, Classical Petri Nets: Introduction, Formal Definition of Structure, Behavior, Examples. Slides	Lecture Notes Sections 7.1-7.6 Book Section 4.4 on aggregate functions.
7	October 29	Modeling, Role of Tokens, Places and Transitions, Typical Network Structures, Applications of Petri Nets in Bioinformatics: Metabolic Pathways, Genetic Regulatory Networks. Slides	Lecture Notes Sections 7.7, 7.9, additional lecture notes: Modeling Genetic Networks with Petri Nets
8	November 1	Examples of modeling biological networks with Petri nets. Modeling different behaviors: oscillations and steady states. Genetic switch. Natural and man-made genetic oscillators: Circadian Clock. Repressilator. Slides.	Biological clock (another reference to the Circadian Clock)
9	November 5	Evaluation and discussion of Part A of the Term Project. Back to SQL: Inner Join. Boolean networks as models of biological networks. Comparison of biological networks to random networks. Common patterns (subparts) of the networks, Motifs. Slides.	Modeling genetic networks with Boolean functions
10	November 8	Different variants of the Feed-Farward Loop motif. Boolean regulatory graphs. Dynamics and functions of the Feed-Forward Loop motifs. SQL embedded in Java. Demos: MySQL client on the Reactome database. Petri-net editor Yasper. Examples in Yasper: Activation, Inhibition, Positive Feedback Circuit, Negative Feedback Circuit. Slides.	Book Chapter 5 (Embedded SQL)

Acknowledgments:

Most of the contents (slides, exercises, exams) on this page is based on material provided by Nico Kuijpers and Geert-Jan Houben.