GENERAL CONTACT

Dr. Eric R. Geertsma
Junior Professor
Biocenter N200/1.08
Phone +49-(0)69-798-29255
F
ax: +49-(0)69-798 29244

Email

Beate Braungart
Administrative assistant
Biocenter N200/1.10
Phone +49-(0)69-798-29238
Fax: +49-(0)69-798 29244

Email

Teaching

Membrane Biology
Biochemistry (M.Sc., lecture, 3 CP). Jun. Prof. Ernst, Jun. Prof. Geertsma
WS2016-2017: mondays from 24.10.2016 until 23.1.2017; between  12:15-13:45; BMLS 2OG Seminar room.

Biological membranes play a central role in both the structure and function of all cells. Not only do they define compartments, they are also responsible for the communication between the inside and outside of the cell.  In this module we discus biological membranes from the perspective of their main constituents: lipids and proteins. Topics included are the diversity of lipids and membrane proteins, their biogenesis, interactions, dynamics and medical relevance. Each lecture combines both theory as well as related practical aspects for studying membrane lipids and proteins.
Detailed contents and slides

Python programming for Biochemists
Biochemistry (M.Sc., lecture and practical, part of the Structural Bioinformatics course (6 CP, obligatory module)). Prof. Güntert, Jun. Prof. Geertsma
Summer semester 2016: monday 02.05, 09.05, friday 13.05, monday 30.05, and thursday 09.06 (changed dates!) from 09:00-17:00, Beilstein Computer Center, room A and B.



Need to analyze the entire proteome of a bacterium? Determine the amino acid sequences of the variable regions from many antibody genes? An elementary understanding of programming opens the doors to the analysis of large datasets and the automation of repetitive tasks. In this practical students will learn the basics of the Python programming language; no prior experience is assumed. Python is a versatile and robust language that was explicitly designed to be easy to learn. Python is widely used in the scientific community and very well suited to analyze biological data. Finally, knowledge of Python will facilitate the understanding of other programming languages as well. This practical combines lectures and exercises in which students write programs of gradual increasing complexity.


Python is free and available for all common operating systems (see python.org). The course loosely follows the book “Python for Biologists” from Dr. Martin Jones (partly available online at pythonforbiologists.com) and the Biopython tutorial (available online at biopython.org). The first three days, new topics and concepts are introduced in lectures and subsequently practiced by exercises. The acquired knowledge is tested with a small programming project on day 5. The (well-commented) Python script of the final project serves as an intermediate report, questions related to Python will be part of the final exam of the Structural Bioinformatics course. Computers will be available but participants are encouraged to bring their own computer.

Day 1: Introduction into programming, the Python language and its software environment, writing and running your first python script, storing and manipulating data in text strings and lists. Day 2: Storing and manipulating data in dictionaries, repeating actions with loops, functions. Day 3: decision making using conditional statements, reading and writing files, searching for patterns using regular expressions. Day 4: Biopython. Day 5: Wrap-up and exam.