Agents in Biology
187
FIGURE 7.4: Calling Copasi from FLAME C code.
other toolkits and languages better than writing them as C functions. For this
purpose, it makes sense for the simulation code in C to halt and call other
toolkits, receive the results and then progress with the results. In this case
COPASI was called through C commands to complete part of the simulation
work (Figure 7.4). This method can also be merged with MATLAB and other
toolkits when doing complex matrix calculations which are cumbersome to do
in the C language.
7.3 Modeling Drosophila Embryo Development
In this experiment, two models of the same phenomenon were compared -
one written using stochastic methodology in MATLAB and other using agentbased modeling. The Bicoid morphogen gradient establishment takes place
during early embryo development in Drosophila melanogaster, and is a dynamic system that allows the Bicoid molecules to diffuse along the embryo
anterior-posterior (A-P) axis in different developmental stages. The protein
concentration gradient is sensed by downstream genes and induces differential
spatial pattern of gene expression. In most analyses of this process, the bicoid
mRNA is thought to supply proteins at a constant rate in the anterior pole of
embryo. Based on these experimental evidences, Liu and Niranjan [120] proposed three Bicoid concentration computational models in which the maternal
bicoid mRNA is regulated by being held constant for 2 hours and followed by
rapid decay. The uncertainty of such source regulation model is also verified
later by Gaussian processing in [121].
In this work, two approaches of modeling Bicoid morphogen concentration gradient are compared. The first approach, stochastic chemical reaction
system [120, 121], models the propagation of the diffusion rate of changes
using the stochastic modeling in MATLAB software. Another model in agentbased modeling using FLAME is implemented to compare the results and the
problems faced in both modeling approaches.
187
FIGURE 7.4: Calling Copasi from FLAME C code.
other toolkits and languages better than writing them as C functions. For this
purpose, it makes sense for the simulation code in C to halt and call other
toolkits, receive the results and then progress with the results. In this case
COPASI was called through C commands to complete part of the simulation
work (Figure 7.4). This method can also be merged with MATLAB and other
toolkits when doing complex matrix calculations which are cumbersome to do
in the C language.
7.3 Modeling Drosophila Embryo Development
In this experiment, two models of the same phenomenon were compared -
one written using stochastic methodology in MATLAB and other using agentbased modeling. The Bicoid morphogen gradient establishment takes place
during early embryo development in Drosophila melanogaster, and is a dynamic system that allows the Bicoid molecules to diffuse along the embryo
anterior-posterior (A-P) axis in different developmental stages. The protein
concentration gradient is sensed by downstream genes and induces differential
spatial pattern of gene expression. In most analyses of this process, the bicoid
mRNA is thought to supply proteins at a constant rate in the anterior pole of
embryo. Based on these experimental evidences, Liu and Niranjan [120] proposed three Bicoid concentration computational models in which the maternal
bicoid mRNA is regulated by being held constant for 2 hours and followed by
rapid decay. The uncertainty of such source regulation model is also verified
later by Gaussian processing in [121].
In this work, two approaches of modeling Bicoid morphogen concentration gradient are compared. The first approach, stochastic chemical reaction
system [120, 121], models the propagation of the diffusion rate of changes
using the stochastic modeling in MATLAB software. Another model in agentbased modeling using FLAME is implemented to compare the results and the
problems faced in both modeling approaches.