max planck institut
informatik
informatik
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")
| 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). |
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 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 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 |