Practical course Network and Expression data analysis (SS2016, NEAP)

• Room:A 406 + CIP-pool, Amalienstr. 17
• Start and introduction: Tuesday,19.04.2016 14:00, A 406
• Date (during the semester): Tuesday (14:00-18:00) and Thursday (14:00-18:00)
• Semester break: 2 week block course 18.07.-29.07.2016 / 1.8.2016
• Credits:: 10 SWS / 12 ECTS (10P/Block)

At the beginning of the semester all required material will be provided at the interal Webpage (Internal web page)

The topic of the course is a certain disease model: Atheorsclerosis (the main problem in cardio-vascular diseases).

In the course, we will derive network models to compile all available knowledge about the disease in the form of unified networks (Petri nets). For this we will employ database extraction and text mining using tools developed in the group. Methods for the application case Atherosclerosis will be improved and new methods will be implemented.

In addition, we will develop a 'big data index' compiling all the high-throughput data sets relevant for atherosclerosis and develop a web-based tool to access, search and index these datasets.

The resulting network (Atheronetwork) and data index (Atheroindex) should be usable in reaserach projects on Atherosclerosis together with medical groups to interpret their datasets.

This will in particular include NGS data sets such as RNA-seq and sRNA-seq, microarray, miRNA and proteomics/mass spec data sets.

The course has three parts:

1. Seminar and methods
2. Implementation of a novel approach
3. Application to current data and writing of manuscript

Please note: During the seminar part, talks might take place on tuesday and thursday to speed up the basic introduction

• Prof. Dr. Ralf Zimmer
• Dr. Gergely Csaba
• Dr. Florian Erhard

• Bachelor Bioinformatics
• Bioinformatics programming course
• Practical Genome-oriented bioinformatics

Good programming skills in Java under Linux will be required. The practical course will be performed in small groups of 3-4 students.

1. Seminar talks
2. Exam on the web-based system for Atheronetwork an Atheroindex
3. Report, manuscript or paper