Cancer 2013 May (2)-5

 

ELECANS – An integrated model development environment for multiscale cancer systems biology.

Bioinformatics. 2013 Apr 1;29(7):957-9

Chaudhary, S. U., Shin, S.-Y., Lee, D., Song, J.-H., and Cho, K.-H.*

Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea. http://sbie.kaist.ac.kr

Abstract

(http://sbie.kaist.ac.kr/)

Motivation: Computational multiscale models help cancer biologists to study the spatiotemporal dynamics of complex biological systems and to reveal the underlying mechanism of emergent properties.

Results: To facilitate the construction of such models, we have developed a next generation modelling platform for cancer systems biology, termed ‘ELECANS’ (electronic cancer system). It is equipped with a graphical user interface-based development environment for multiscale modelling along with a software development kit such that hierarchically complex biological systems can be conveniently modelled and simulated by using the graphical user interface/software development kit combination. Associated software accessories can also help users to perform post-processing of the simulation data for visualization and further analysis.

Conclusions: In summary, ELECANS is a new modelling platform for cancer systems biology and provides a convenient and flexible modelling and simulation environment that is particularly useful for those without an intensive programming background.

 

Additional Information

Multiscale modeling in cancer systems biology involves a systematic integration of various biological models of different scales to investigate the system-level properties such as those defined as “hallmarks of cancer”. The multiscale models include sub-cellular gene regulatory network models, cell cycle models, extracellular biochemical interaction models, and tissue-level cell interaction models. Figure 1 shows the typical modeling schema for multiscale modelling.

ELECANS not only provides a comprehensive modelling coverage of various scales, but also allows flexible coupling across such different scales for complex and highly specific investigation scenarios. The modelling methodology for each of the aforementioned sub-models varies depending on the modelling scenario requirements. To accommodate these, .NET based user code editors in ELECANS allow Boolean modelling, rule-based modelling as well as ordinary differential equation modelling of the gene regulatory networks as well as the cell cycle.

Another special feature of ELECANS is that its graphical modelling studio is supplemented by an application programming interface and an associated software development kit. This imparts re-programmability to the ELECANS middleware which can facilitate users to rewrite, optimize or update the internal algorithms and methods.

The software design of ELECANS is based on a combination of legacy and state of the art design patterns which not only increase the reliability of the software but also render it scalable and customizable. A modular layout of this architecture is shown in Figure 2. Modelers can adapt this architecture or its variations to improve the overall quality of their own multiscale modelling platforms.

Fig 1

Kwang-hyun Cho-1png

Fig 2

Kwang-hyun Cho-2png

 

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