Information Technology Reference
In-Depth Information
OpenGL extension which provides an additional application programming in-
terface (API) enabling GTK+ widgets to rapidly render scenes rapidly using
OpenGL's graphics acceleration capabilities. Capture of the simulation run to
a movie file requires the software Transcode [30] and the desired compression
codecs be installed on the user's machine.
For non-graphical batch runs, a command-line interface,
logmasyv
,isalso
implemented. This option is designed to run multiple simulation runs (e.g. for
parameter sweeps on large computer grids). This option requires only that a
C compiler be available, and it eliminates the substantial CPU overhead cost
incurred by the graphical services. Communication between the server program
(either
masyv
or
logmasyv
) and the client simulation is done through a Unix
domain socket stream.
MASyV is open source software distributed under the GNU General Public
License (GNU GPL) and is freely available for download from SourceForge [31].
It has a fixed web address, it is well maintained and documented, has an on-
line tutorial, and comes with a “Hello World” client simulation demonstrating
how to implement a new client and how to make use of the message passing
library. MASyV also comes with a few example pre-programmed clients such as
an ant colony laying and following pheromone trails (
ma ants
) and a localized
viral infection (
ma immune
) which was used in [11,32]. Our influenza model was
derived from
ma immune
and is now distributed with MASyV under the name
ma virions
.
7Con lu on
We have described the implementation of an agent-based simulation built to re-
produce the dynamics of the in vitro infection of a lung epithelial cell monolayer
with an influenza A virus. At this time, model development is still in its pre-
liminary stage, and many details remain to be elucidated. However, preliminary
runs with biologically realistic parameter values have yielded reasonable results
when compared with the currently available experimental data.
Recent results from the in vitro experiments revealed that large numbers
of virions were being trapped by the mucus. While at 1 h post-harvest viral
assays revealed that the experimental well contained about 4
,
701
±
180 virions,
it contains a mere 635
240
virions at 4 h post-harvest. These new results suggest that trapping of the virions
by the mucus and the absorption of virions by the epithelial cells upon infection
plays a crucial role in controlling the rate of spread of the viral infection. In
light of these new results, we plan to direct our future research towards better
characterizing the role of the mucus in viral trapping and its effect on viral
infectivity.
This recent development is an excellent example of just how much we still need
to learn about influenza infection. It also shows that our strategy of combining
in vitro and in silico tools will prove a useful tool in this quest.
±
273 virions only 1 h later at 2 h post-harvest and 720
±
