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