INTERACTIVE VISUALIZATION TOOL

FOR TUMOR GROWTH SIMULATIONS

Rafal Wcislo

Department of Computer Science, AGH University of Science and Technology, Cracow, Poland

Keywords:

Simulation, Visualization, Tumor growth, Angiogenesis.

Abstract:

We present the main requirements and ready-to-use components of the interactive visualization tool for mod-

eling of solid tumor proliferation. As the simulation engine it uses complex automata paradigm, which inte-

grates cellular automata with particle dynamics. To make it sufﬁciently fast for interactive visualization we

show that the system can be efﬁciently implemented on multicore workstations, with moderate number of pro-

cessors controlled by data parallel interface such as OpenMP. In the near future the system will be empowered

by a combined CPU and GPU computational environment. This in silico lab system is intended for medical

laboratories doing research in oncology and/or in anticancer drug design.

1 INTRODUCTION

There are many mathematical models of tumor

growth driven by the process of angiogenesis (Folk-

man, 1971; Castorina et al., 2009; Bellomo et al.,

2003; Chaplain, 2000; Preziozi, 2003; Mantzaris

et al., 2004; Lowengrub et al., 2010). The models fall

into four categories: (a) continuum models that treat

the endothelial cell (EC) and chemical species den-

sities as continuous variables that evolve according

to a reaction-diffusion system, (b) mechano-chemical

models that incorporate some of the mechanical ef-

fects of EC-ECM (extracellular matrix) interactions

els in which cells are treated as units which grow

and divide according to prescribed rules (d) hybrid

multiscale models involving processes from micro-to-

macroscale. Multiscale and multiphysic models rep-

resent the most advanced simulation methodologies.

In (Wcislo et al., 2009) we present the concept of

tumor growth model which is driven by particle dy-

namics (Haile, 1992; Dzwinel et al., 1999; Dzwinel

et al., 2000; Dzwinel et al., 2006; Kadau et al., 2004)

combined with a cellular automata paradigm (Hoek-

stra et al., 2007; Sloot and Kroc, 2009). In this article

we present a tool used for preparation and visualiza-

tion of such a simulation. At a certain stage the cre-

ation of that tool became crucial due to:

• A number of simulation parameters (physical as

well as chemical and biological characteristics of

tissues are deﬁned by as many as a few dozen up

to a few hundred of parameters) which became

very inconvenient to modify manually in the text

ﬁle.

• The simulation is expected to consist of several

million of particles (depending on the modeling

there shall be either single cells or their clus-

ters together with the ECM) forming a three-

dimensional fragment consisting of a healthy tis-

sue, an array of blood vessels and a tumor. Thus

a tool that would make it possible to interactively

observe such a simulation would undoubtedly be-

come a signiﬁcant aid for a researcher.

2 VISUALIZATION TOOL

Figure 1 presents the view of the main screen of the

visualization program.

2.1 Tissue Templates

The simulation program allows several types of tis-

sues to be present simultaneously (a typical situation

in the simulation is when there is a cancerous tissue

surrounded by a healthy one and the two are interwo-

ven with the network of blood vessels). Each tissue

has an array of characteristic features such as density,

an average size of cells, the rate of diffusion of partic-

ular substances (oxygen, TAF), oxygen requirements,

life span, resistance to oxygen deﬁciency, etc.

270

Wcislo R..

INTERACTIVE VISUALIZATION TOOL FOR TUMOR GROWTH SIMULATIONS.

DOI: 10.5220/0003131402700273

In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS-2011), pages 270-273

ISBN: 978-989-8425-36-2

 2011 SCITEPRESS (Science and Technology Publications, Lda.)

Figure 1: The main window of the visualization program.

The tool has already prepared predeﬁned sets of

data for chosen tissues so it is not necessary to de-

ﬁne all the parameters every time for a certain tis-

sue. These sets are prepared on the grounds of the

biomedical data. During the preparatory stage when

the user of this program deals with the initial values

of the simulation, the data might be easily loaded and,

subsequently, each parameter may be modiﬁed. This

modiﬁed set of the parameters might also be saved as

a template for other simulations.

2.2 Position, Rotation, Size

Due to the fact that it is impossible to reconstruct

properly a process of blood vessel formation (angio-

genesis) in two dimensions, all the simulations are

currently carried out in three dimensions. 3D makes

the simulation more accurate and consistent with re-

ality; however, it signiﬁcantly increases the time of

computation and it complicates the way of deﬁning

initial tissue shape and location.

The discussed visualization tool makes it easy to

position the tissues as well as adjust their size, lo-

cation and space orientation so that the creation of

an initial simulation state is facilitated. Such opera-

tions are mostly performed with the help of a com-

puter mouse and a few keyboard shortcuts and func-

tion keys. The program allows the user to watch the

prepared simulation from each side, zoom it, etc.

2.3 Simulation

As soon as the simulation is prepared, the program

makes it possible to run the simulation. It might

be run either on the single-processor computers as

well as on multi-processor ones equipped with a

shared memory (then the simulation program uses the

OpenMP libraries). Due to the parallel execution, the

time of calculation of particular steps is shortened

and, therefore, the simulation is accelerated and the

results are obtained earlier. At present, the research is

being carried out over the implementation of the sim-

ulation on GPU devices.

If the simulation is performed locally, it might be

watched on-line (Fig. 2). In that case the program

shows the information concerning particular tissues

(e.g. the number of cells, the number of cells in vari-

ous states, pressure, O

concentration). The program

allows to watch the tissues from any angle as well as

make random cuts so that it is possible to have an in-

sight into a tissue interior.

The visualization program makes optimizations

that allow to watch the simulations - even those con-

sisting of hundreds of thousands of particles - ﬂuently.

INTERACTIVE VISUALIZATION TOOL FOR TUMOR GROWTH SIMULATIONS

271

Figure 2: Simulation visualization. Normal cells are marked in white, tumor cells – in red. Tissue section is visible.

It is also possible due to the fact that it has the access

to all the parameters of the simulation. This program,

thus, holds an advantage over other visualization pro-

grams intended for general use.

3 CONCLUSIONS

It should be taken into account that during the creation

of simulation programs, tools that could be used con-

secutively in in silico experiments should also be pre-

pared. It is particularly crucial in the case of prepar-

ing a simulation of complex processes during which it

is necessary to deal with hundreds of parameters and

analyze the results from various dimensions. Such

a convenient and intuitive tool allows to do the re-

search undoubtedly more effectively as well as to ver-

ify one’s hypothesis quicker.

ACKNOWLEDGEMENTS

This research is ﬁnanced by the Polish Min-

istry of Higher Education and Science, project

N N519 579338 and partially by AGH grant

No. 11.11.120.865.

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