Graph-based modeling of biochemical system

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Szárnyas Gábor
Department of Measurement and Information Systems

In the last decades, the use of informatical solutions has begun to spread in biochemical research. They started to simulate these models in IT systems to help draw conclusion, not just by making physical measurements.

However, data storing and processing have not yet been provided with unified and effective tools. The data is available in a large variety of formats, and requires a different approach and a different way of thinking to process. Storing and processing these data means new IT challenges.

The purpose of my thesis is to process the data of a model of molecules and molecule interaction and to simulate these interactions. Organize the data efficiently into graph database and transform the molecule interactions into graph transformations. Examine the performance and accuracy of the simulations.

In my thesis, I mapped the biochemical model into a graph database where it is possible to carry out the graph transformations corresponding to the chemical reactions in the molecule model. I simulated the transformation steps. I measured the performance of the transformations and checked the accuracy of the simulation by measurement.

The graph database not only enables the visualization of transformation results, but also the database itself. The molecules can be well represented, and the results of each transformation appears in the database. This way, the transformations are easy to test. Chemical reactions which cannot be defined in the biochemical model of BioNetGen, due to the greater expression power of the query language of the graph database, are possible to describe with this process.


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