Projects --

You can find more of my projects at, not all are listed here.


The Visualization of Protein Ligand Graphs (VPLG) software

The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm.

The project page with an introduction to the software is at and you can find the source code at

Created with: Java SE, PostgreSQL, NetBeans IDE, Ant, Subversion, Git

The Protein Topology Graph Library (PTGL) web server

The PTGL web server provides a database of protein secondary structure topologies. It is based on protein ligand graphs and other data computed by the VPLG software. The PTGL uses a graph-based model to describe the structure of proteins on the super-secondary structure level. The web server allows you to search for protein motifs which can be detected in the graphs. It also provides standardized 2D visualizations of protein graphs and folding graphs. In contrast to the manually curated CATH and SCOP databases, the method used by this server is fully automated.

The PTGL is run by the Molecular Bioinformatics group of Ina Koch at Goethe-University Frankfurt am Main, Germany. The server can be accessed at

Created with: PHP, JavaScript, HTML/CSS, PostgreSQL, NetBeans, Subversion, Git, Apache, Bash, OpenPBS

Publication: Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, and Ina Koch. The new Protein Topology Graph Library web server. Bioinformatics, 32(3):474–476, 2016. Link

Business Backend

The website is a search engine and price comparison tool for long-distance bus rides in Germany. I designed the database and wrote the major part of the backend which is responsible for retrieving data on bus rides from the APIs of different bus companies. (Update 2016: The website is no longer operational.)

Created with: PHP, MySQL, JavaScript, HTML/CSS

Just for fun: Visualization and Game dev

PRace (Mini game in Javascript/Processing.js)

PRace is a HTML mini arcade game that can is played by pressing and releasing a single button. You are a small space ship in a cave and have to evade enemies, but flying close to them scores you points. You can find more info and give it a shot here with a modern browser.

Created with: Processing.js, JavaScript, HTML/CSS


LivePlot (Visualization)

This is a visualisation of random data as a 2-D line plot. An increasing number of lines are plotted in 2D. By default, each lines randomly selects new y values, but you can place the mouse into the scene to attract the lines to the cursor's y position with a certain probability.You can try it live at the p5js web editor (just click the play button at the top).

Created with: p5js



Way2Close is a multi-platform implementation of the PRace idea, written in C# and based on the Unity engine. It's in alpha stage and you can grab Android packages in the releases section at Github. It could use sounds and some more levels, but it's already playable in the current state.

Created with: Unity, C#, VisualStudio, Git

Code and releases: