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Max-Planck-Institut für Informatik
max planck institut
mpii logo Minerva of the Max Planck Society

Biological Networks: Databases and Analysis Methods (SS 2008)

General Outline:

The lecture will introduce fundamentals of relational databases and teach bioinformatics methods for analyzing molecular interaction networks with a special focus on human networks and diseases. The lecture topics will be similar to last year's lecture. No extra enrollment is required, but you should subscribe to the lecture mailing list for important announcements like lecture time changes and the availability of a new homework assignment sheet; to subscribe, send an e-mail to bionetYEAR@mpi-inf.mpg.de (replace YEAR by 08) with the following information: your first and last name, matriculation number, semester number, bachelor or master, BI or CMB student, Helm's Bioinformatics III lecture attended or not, Koch's database lecture attended or not (attendance of these other lectures is no prerequisite, it is just for our information). Click here for the official entry of this lecture in the lecture directory ("Vorlesungsverzeichnis"). All CS lectures of this summer semester are listed here.

Lecturer: Dr. Mario Albrecht
Tutorial Coordinator: Dorothea Emig
Tutors: Dorothea Emig, Alejandro Pironti, Hagen Blankenburg, Fidel Ramírez, Andreas Schlicker

Rating: 5 credit points ("Leistungspunkte") for special lecture ("Spezialvorlesung")
Language: German and English

Time and Location (detailed schedule and exceptions below):

First Lecture: 17 April 2008
Last Lecture: 10 July 2008
Exam: 14 July 2008

Lectures: Thursdays, 10:15-12:45, MPII building E1.4, Room 024.
Tutorials: Biweekly (on Thursdays, 13:00-14:00), MPII building E1.4, Rotunda 5th floor.
Examination: Written exam on Monday, 14 July 2008, 10:15 s.t., Department of Mathematics E2.5, Lecture room IV (Hörsaal IV)
Office hours: Dorothea Emig, Mondays, 14:00-15:00, MPII building E1.4, Room 521 (or by appointment).
Dr. Mario Albrecht, after each lecture (or by appointment, MPII building E1.4, Room 527).

Target Group and Prerequisites:

The lecture is targeted to advanced bachelor and master students of bioinformatics.

Requirements for the Final Examination and Certificate:

Each of the 5 homework assignments has 60 points. At least half of the points from all assignments (150 points) are required to qualify for the final written examination. Grade of certification ("Schein") is based on the final exam only.

Homework assignments will be made available after each lecture on this web page. Please return your solutions by the given date in time. You can submit solutions in groups of up to two students.

The general procedure for the assignment submissions is as follows:
The complete solution (inclusive source code & command line syntax if necessary) must be submitted in written form to the box in the first row of the lecture room. If you cannot come to the lecture, you have to submit your solution before the lecture starts to Dorothea in room 521 or at least to our secretary in room 502. In addition, for all programming exercises, the interpretable or compilable source code (and an executable program if compilable) must be sent to us by e-mail.

We strongly encourage you to submit computer-printed solutions. In case you want to submit hand-written text, please note that we can only grade neat and easily readable sheets.

Importantly, please always read the assignment sheets very carefully because there may be deviations from these general rules in some cases.

Lecture and Tutorial Downloads:

Contents: Tentative Lecture and Tutorial Schedule (subject to change!)

Lecture No. Date Main Topics Reading (apart from other material) Assignment No. Assignment Due
Lecture 1 Thursday, April 17 Overview and Introduction to Database Design Kemper's Chapters 1 - 2.7 - -
Lecture 2 Thursday, April 24 Database Design, Ontologies, Relational Modeling Kemper's Chapters 2.8-2.12, 3.1-3.4.6 - -
No lecture Thursday, May 1 Public holiday - Assignment 1 Thursday, May 15
Lecture 3 Thursday, May 8 Relational Algebra and SQL Kemper's Chapters 3.1-3.4.11, 3.6 and 4.1-4.8, 4.13, 4.15 - -
Lecture 4 Thursday, May 15 Advanced SQL and Data Integrity Kemper's Chapters 4.9-4.12, 4.16-4.21 and 5 Assignment 2 Thursday, May 29
No lecture Thursday, May 22 Public holiday - - -
Lecture 5 Thursday, May 29 Functional Dependencies and Normalization Kemper's Chapter 6.1-6.3.0, 6.4-6.9, 6.12 Assignment 3 Thursday, June 12
Lecture 6 Thursday, June 5 Introduction to Network Types Hu, Nat. Biotechnol., 2007; Barabasi, Sci. Am./SdW, 2003/4; movies are optional - -
Lecture 7 Thursday, June 12 Network Definitions and Topology Barabasi, Nat. Rev. Genet., 2004: 101-106; Albert, J. Cell Sci., 2005: 4947-4949; Zhu, Genes Dev., 2007: 1010-1016; rest is optional Assignment 4 Thursday, June 26
Lecture 8 Thursday, June 19 Integrative Systems Biology I, Functional Similarity Measures Ng, Brief. Bioinf., 2006; Schlicker, Nucleic Acids Res., 2008; Schlicker, BMC Bioinf., 2006: Background (1-3) & Methods (12-14); Assenov, Bioinformatics, 2008; rest is optional - -
Lecture 9 Thursday, June 26 Integrative Systems Biology II, Network Topology Applications, Diseasome Almaas, J. Exp. Biol., 2007: 1548-1551; Rubinsztein, Genome Biol., 2006; Goh, PNAS, 2007; rest is optional Assignment 5 Monday, July 7
Lecture 10 Thursday, July 3 Alternative Splicing and Protein Domain Interactions Blencowe, Cell, 2006: Figures 1 & 2 (37-39); Riley, Genome Biol., 2005; rest is optional - -
Lecture 11 Thursday, July 10 Drug and Disease Networks and Disease Gene Prioritization Yildirim, Nat. Biotechnol., 2007: 1119-1124; Oti, Clin. Genet., 2007: Figures 1 and 3; Franke, Am. J. Hum. Genet., 2006; rest is optional - -
No lecture Thursday, July 17 None - - -

Tutorial Date Topic
Tutorial 1 Thursday, May 8 Examples
Tutorial 2.1 Thursday, May 15 Assignment 1
Tutorial 2.2 Thursday, May 29 Assignment 1
Tutorial 3 Thursday, June 5 Assignment 2
Tutorial 4 Thursday, June 19 Assignment 3
Tutorial 5 Thursday, July 3 Assignment 4
Tutorial 6 Thursday, July 10 Assignment 5

Main Literature List:

MySQL Software List:

Optional Literature List (Semesterapparat):

Optional SQL Literature List: