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

Seminar Computational Systems Medicine (SS 2011)

General Information

Lecturer: Dr. Mario Albrecht
Tutors: Hagen Blankenburg, Nadezhda T. Doncheva, Fidel Ramírez, Sven-Eric Schelhorn
Language: English

Important Dates

Submission of handout draft and preliminary talk slides: Wednesday, 22 June 2011
Seminar schedule (details below): 7-13 July 2011
Location of all seminar talks from 7 to 13 July: Rotunda room 533 on the 5th floor in the Max Planck Institute for Informatics, Campus E1.4, Saarbrücken
Location of guest talk on 13 July 2011 at 17:00: Lecture room 001 in the CBI building, Campus E2.1, Saarland University, Saarbrücken


This seminar can be attended by bachelor students (worth 5 CP) and master students (worth 7 CP) of bioinformatics. The language is English. The final schedule for the seminar will be decided in June.

For a successful seminar completion, every student is required to:

  1. Read about the topic assigned by the tutor. The tutor provides the student with few main publications about the talk topic, but the student is encouraged to look for additional information in the scientific literature. To some extent the student can also negotiate the concrete topic with the tutor. The student should be selective and restrict his talk to some part of the information covered by the publications.
  2. Write a handout on the topic in English. Bachelor students have to write 1.5-2 pages of text summarizing the talk contents. Master students have to write 2.5-3 pages of text summarizing the talk contents. The handout (page size DIN A4, page margins 2.5 cm, font Times, 12 pt, single-line spacing) has to cite primary information sources and literature references. It may contain some bullet points and additionally at most one insightful figure (size of at most half a page). The strict deadline for handout submission to both the lecturer and the tutor is Wednesday, 22 June 2011. The student will then receive feedback from the tutor before the talk. The tutor will print the handout for the seminar.
  3. Contact and meet your tutor well before the final talk. Every student can (and is encouraged to) communicate with the tutor and has to schedule a meeting with the tutor to discuss the topic, the handout and the talk slides well before the final talk. The handout draft and prefinal talk slides have to be submitted to both the lecturer and the tutor by Wednesday, 22 June 2011.
  4. Prepare and give a talk on the assigned topic in English. Bachelor students have to give a talk of 25-30 min. Master students have to give a talk of 40-45 min. Every talk is followed by a short discussion in English.
  5. Participate actively in the whole seminar and the discussions after the talks. Each student has to attend all seminar talks and must inform both the lecturer and the tutor in case of unavoidable absence.
  6. Submit the final handout and talk slides. Each student has to submit the finalized handout 1 day before the seminar talk. The final handout updated based on the feedback received during the talk as well as the finalized talk slides have to be submitted 1-2 days after the talk. The handout has to be a single PDF. The talk slides should be submitted in PPT or PPTX or ODP (other file formats on request, just contact the lecturer).
  7. Deliver a scientifically reasonable handout and talk. The quality and contents of both the handout and the talk will be assessed, see presentation guidelines and useful advice below.

Presentation guidelines for seminar talks

Professor Lengauer provides guidelines for scientific presentations. They are available in English (DOC or PDF) and in German (DOC or PDF). They are really helpful! Please read them carefully before you start working on our talk slides.

Useful advice for seminar talks

Seminar Material

One publication relevant to the whole seminar is by Wist, A.D. and colleagues.

Further publications for each talk topic are available in this password-protected area.

Seminar Topics

Date Time Topic
07 July 2011 13:00 Flux balance analysis for systems medicine
08 July 2011 13:00 Human disease classification and networks
08 July 2011 14:00 Interaction networks and disease
08 July 2011 15:00 Disease pathway identification using RNAi
11 July 2011 12:00 Network-based drug discovery
11 July 2011 13:00 Clinical biomarker discovery
12 July 2011 16:00 Cause-effect relationships in medicine
13 July 2011 13:00 Human gene expression using RNA-Seq
13 July 2011 16:00 The role of miRNAs in human disease
13 July 2011 17:00 Dynamic regulatory networks of gene expression