From the 22.04.2003 until the 31.03.2004 I participated in a one year postgraduate course in bioinformatics at the Cologne University BioInformatics Center. In this course were scientists, who have an educational background in life sciences, mathematics or computer science.

Basics in Computer Science and Mathematics Programming Course Python (48h) Introduction to the main language concepts Data types Expressions Instructions Operators Exceptions Control Flow Modules and programs Introduction to object oriented programming Classes and objects Attributes, methods Inheritance, multiple inheritance Memory management File management User interfaces Distributed objects Python and the internet Data Structures (24h) Runtime of algorithms/ Complexity theory Representation of numbers in a computer Simple data structures Arrays Lists Queue Stack Tree Sorting Quicksort Heapsort Bucketsort Searching Software Engineering (12h) Editors Makefiles Debugger Browser Profiler Fundamental software engineering concepts Version control (CVS) Unified modeling language (UML) Development chain management (IDE) Unix (24h) Basics System administration Databases (24h) Fundamental concepts Relational databases Object oriented databases Biological databases Internet (24h) Introduction Adressing/TCP/IP Services Telnet FTP WWW HTML Applets Structured data formats XML XHTML Corba Networks and Parallel Computing (12h) Protocols Topologies Distributed computing Message passing Cluster Security aspects Graph Theory (12h) Directed and undirected graphs Representation on graphs in a computer Connected components Paths Cuts Cluster Algorithms for graphs Linear Algebra (36h) Vectors and matrices Solving systems of linear equations Coordinate transformations in vector spaces Linear models and linear programming Combinatorics (24h) Counting and combinatorial configurations Combinations Permutations Binomial theorem Urn models Induction Analysis and Numerics (24h) Norm and length measurements in vector spaces Differentiability Nonlinear optimization and systems of nonlinear equations Interpolation with polynomes (splines) Linear and nonlinear regression Statistics (30h) Random variables Simple statistical models (independent variables) Distributions Gauss Binomial Geometric Conditional probabilities, Bayes´theorem Parameter estimation Bayes Maximum likelihood Markov-Models HMM´s Hypothesis testing Model Construction and Heuristics (18h) Graph theoretic approaches Petri nets Local search strategies Gradient descent Simulated annealing Monte Carlo simulation

Applied Bioinformatics Installation of a Linux PC (24h) Administration Security Databases (MySQL, Access, objectoriented databases) Sequence Alignment (24h) Dot plots Needleman-Wunsch Smith-Waterman Similarity matrices Penalties Statistics of gene- and protein alignments Multiple Sequence Alignment (24h) ClustalW Pileup Clustering methods and principles Phylogenetic trees RNA-Secondary structure prediction Quick Sequence Searches in Databases (24h) Blast and derivates FASTA PSI-BLAST & Hidden Markov models BLAT Genome Analysis (48h) Data analysis Annotation Gene Prediction (prokaryotic, eukaryotic, promoter prediction, transcription factor binding sites) Protein function prediction Genome comparison Neural networks Proteomics & Transcriptomics (24h) Pattern recognition DNA-Chips 2D-Gele Mass spectrometry Protein-Protein interaction Protein Structure (24h) Visualisation & Modelling Secondary structure prediction Localization/Hydrophobicity Analysis of domains Folding classes, families and domains 3D-Alignment Force Field and MO Methods (24h) Structure optimization, algorithms optimization Molecular dynamics & Monte Carlo methods MO-methods QM/MM Homology Modelling (24h) Improvement of alignments Loop prediction, side chain orientation Optimization Quality assessment of protein structure models Threading & ab initio protein structure prediction Rational Protein- and Drug-Design (24h) Stabilization Substrate specificity Humanisation of antibodies Rational drug-design (QSAR, pharmacophores, diversity, ADME prediction) Protein/Protein Docking & Protein/Ligand Docking Coding of Chemical Reactions (24h) Simulation of metabolic pathways Stoichiometrical models (Flux Balance Analysis, Petrinets) Kinetic models (differential equation, coloured Petrinets) Literature Evaluation, Word Analysis (24h)

Project

From November 2003 to April 2004 (20 weeks)
I worked on the practical research-oriented project:
HyDaBa – Hydrogenase Database
at the University of Cologne, Institute for Genetics