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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 2007)

General Outline:

The lecture will both introduce fundamentals of relational databases and teach bioinformatics methods for analyzing molecular interaction networks. 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 us 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 (previous attendance of these lectures is no prerequisite). Click here for the official entry of this lecture in the lecture directory ("Vorlesungsverzeichnis").

Lecturer: Dr. Mario Albrecht
Tutorial Coordinator: Andreas Schlicker
Tutors: Andreas Schlicker, Hagen Blankenburg, Dorothea Emig, Fidel Ramírez
Number of registered students: ~30

Rating: 5 credit points ("Leistungspunkte") for special lecture ("Spezialvorlesung")

Time and Location (detailed schedule and exceptions below):

Lectures: Thursdays, 11:15-13:00, MPII building E1 4, Room 024.
Tutorials: Biweekly, Tuesdays, 11:15-12:45, MPII building E1 4, Room 024.
Examination: Written exam on Monday, 16 July 2007, 13:00-15:00, Department of Mathematics E2 5, Lecture room II (Hörsaal II).
Office hours: Andreas Schlicker, 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 Andreas in room 521 or at least to our secretary in room 502. In addition, for all programming exercises, the source code and an executable version of the program 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 19 Overview and Introduction to Database Design Kemper's Chapters 1 - 2.9 - -
Lecture 2 Thursday, April 26 Database Design and Ontologies Kemper's Chapters 2.10-2.12 Assignment 1.1 Thursday, May 10
Lecture 3 Thursday, May 3 Relational Modeling and Algebra and SQL Kemper's Chapters 3.1-3.4.6 and 4.1-4.7, 4.15 Assignment 1.2 Thursday, May 10
Lecture 4 Thursday, May 10 Joins in Relational Algebra and Advanced SQL Kemper's Chapters 3.4.7-3.4.11, 3.6 and 4.8-4.10, 4.12-4.13 Assignment 2 Thursday, May 24
No lecture Thursday, May 17 Public holiday - - -
Lecture 5 Thursday, May 24 More Advanced SQL and Data Integrity Kemper's Chapters 4.11, 4.16-4.21 and 5 Assignment 3 Monday, June 11
Lecture 6 Thursday, May 31 Functional Dependencies and Normalization Kemper's Chapter 6.1-6.3.0, 6.4-6.9, 6.12 - -
No lecture Thursday, June 7 Public holiday - - -
Lecture 7 Tuesday, June 12 Network Types and Topology Parameters Hu, Nat. Biotechnol., 2007; 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 21
Lecture 8 Thursday, June 21 Domain Networks and Data Quality Schlicker, Bioinformatics, 2007; Blencowe, Cell, 2006: Figures 1 & 2 (37-39); rest is optional Assignment 5 Thursday, July 5
Lecture 9 Thursday, June 28 Functional Similarity Measures Schlicker, BMC Bioinf., 2006: Background (1-3) & Methods (12-14); rest is optional Assignment 5 extra Thursday, July 5
Lecture 10 Thursday, July 5 Disease Gene Networks and Diseasome Almaas, J. Exp. Biol., 2007: 1548-1551; Rubinsztein, Genome Biol., 2006; Goh, PNAS, 2007 - -
Lecture 11 Thursday, July 12 Disease Gene Prioritization and Domain Interaction Prediction Oti, Clin. Genet., 2007: Figures 1 and 3; Franke, Am. J. Hum. Genet., 2006; Riley, Genome Biol., 2005; rest is optional - -
No lecture Thursday, July 19 None - - -

Tutorial Date Topic
Tutorial 1 Thursday, April 26 Examples
Tutorial 2 Tuesday, May 15 Assignment 1
Tutorial 3 Tuesday, May 29 Assignment 2
Tutorial 4 Thursday, June 14 Assignment 3
Tutorial 5 Tuesday, June 26 Assignment 4
Tutorial 6 Tuesday, July 10 Assignment 5

Main Literature List:

MySQL Software List:

Optional Literature List (Semesterapparat):

Optional SQL Literature List: