A new dynamical layout algorithm for complex biochemical reaction networks



Studying complex biochemical pathways in the living cells researchers more and more rely on databases and computational methods. In order to faciliate computational approaches, visualization techniques are highly important. Often biochemical pathways are depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient in the context of biochemical research. One of the main reasons is that there are certain conventions which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. Therefore, a number of approaches has been developed to improve this situation, however, none of them is able to solve the problem well, espescially if highly complex pathways are considered. Out of this reason we have developed a new advanced algorithm which tackles the problem by taking biological conventions into account that have been disregarded so far.

It can also be tested as part of the SimWiz package (free to download for academic users here).

Examples from the publication of the original Becker et al. algorithm.

Examples drawn with the aid of a graphical program.

Examples from the BioCyc database

Examples from the KEGG database

Examples from the PathDB database

Katja Wegner


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