Information Technology Reference
In-Depth Information
4 Distributed Fluorescence Analysis over an Ad-Hoc
Grid/Cloud Infrastructure
This section presents the implemented solution for ecient fluorescence analysis
over an ad-hoc grid/cloud infrastructure.
4.1 Motivation
The final objective of our research is to bring the user of Biomedical or Biol-
ogy fields an easy-to-use tool to complement the analysis of the experimental
data obtained using real microscopes. A cloud-oriented portal for Fluorescence
Microscopy Analysis and related applications will provide an integrated way for
accessing and displaying information to the end user.
Grid/cloud technologies allow to take full advantage of powerful simulation
tools, as the one describing using FCS, without having to follow a complex
installation procedure. This technology will also allow users to access and browse
the obtained data from any mobile device (e.g. smart phone, tablet, etc.).
Furthermore, cloud computing will also provide immediate benefits for exe-
cuting highly computing-demanding fluorescence microscopy simulations in rea-
sonable execution times, by applying HPC techniques over a highly robust com-
puting infrastructure composed of geographically distributed resources. OurGrid
middleware is chosen for it is able to provide a stable infrastructure for executing
BoT applications and is suitable for this article.
4.2 Design and Parallel Model
MCell and FERNet were conceived as sequential applications. MCell produces
the data that is later consumed/processed by FERNet to finally generate the
output (i.e. fluorescence trace) that can be used to analyze the biological process.
The
domain distribution
technique is used as the parallel model for the ap-
plication to be deployed in a distributed environment. No further modifications
are necessary to MCell or FERNet applications. Any UNIX-like computational
platform can execute MCell+FERNet properly. The domain distribution is im-
plemented by partitioning the set of models in a given workload and distributing
them to the available computational resources.
4.3
Implementation in OurGrid
An OurGrid site will provide the environment to execute MCell and FERNet.
The site is composed by a peer, a set of worker nodes and, potentially many
broker/client nodes. The local peer can associate to a community and connect
to other peers. Then, it will be able to share local resources and consume remote
ones.
As described in section 4.2, different subsets containing various instances of
cellular models, possibly from different users, can be created and submitted for
