Biology Reference
In-Depth Information
others had to be consulted. Additionally, we needed a strong network editor, which would be able
to formulate a complete biological system with all its details based on experimental and database
information. Because of the limitation of the software applications we had to develop a new software
application, which we called VANESA.
Modeling the quorum sensing pathway using VANESA
Software solutions, which provide biological network modeling and analysis services, are in high
demand among scientists. It is not surprising that many groups have contributed to the task of developing
software frameworks, which are able to formulate and visualize biological systems. But each software
solution focuses on a particular problem, and none is so powerful that it would be able to address all
problems.
To summarize the situation, different branches of software solutions with different tasks have come
into existence. On the one hand software solutions exist which try to simulate real biological systems
and their processes. Their main task is the representation of a biological system by a mathematical
model. The mathematical language is designed for a precise description of complicated systems. Also
the dynamic processes in biology and their large number of interactions and competing tendencies can
make it difficult to see the whole picture at once. Another problem is the lack of actual laboratory data.
However, in many cases it is not possible to formulate a mathematical system.
Besides the mathematical software solutions, different network modeling frameworks for biology and
medicine were developed. Those frameworks contribute to the task of creating and visualizing biological
systems and networks. Their main focus lies on model management, data integration and data analysis.
Those software solutions provide the possibility to build up biological network models by common
graph representations. Furthermore, they make use of biomedical data sources to extract and integrate
information, which is particular to the topic. The analysis by those software solutions is based on the
network model and the integrated data sets.
Presently it is quite difficult to formulate a sophisticated biological quorum sensing system with the
existing software frameworks. The existing frameworks are not able to capture all relevant elements in
the quorum sensing system. There was a need to develop a software solution that is able to represent
a sophisticated quorum sensing model by an accurate representation. This was the motivation for the
development of the software solution VANESA (
http://vanesa.sf.net
)
.
Using VANESA we started to explore and to extend the quorum sensing network of the model organism
A. salmonicida
. VANESA provides new bioinformatics methods and visualization approaches to analyze
dynamic interacting networks. VANESA is built upon the CardioVINEdb data warehouse [Kormeier
et
al.
, 2009], which provides some of the most important life science databases, such as UniProt, KEGG,
OMIM, GO, ENZYME, BRENDA, PDB, MINT, SCOP, EMBL-Bank, and Pub-Chem [Hariharaputran
et al.
, 2007]. The CardioVINEdb data warehouse was exclusively constructed for the EU project Car-
dioWorkBench. Nowadays, the CardioVINEdb data is integrated into the Data Warehouse Information
System for Metabolic Data (DAWIS-M.D.). DAWIS-M.D. is a platformindependent data warehouse
system that integrates heterogeneous data sources into a local database and provides a comprehensible
updating strategy to ensure a maximum of transparency and up-to-dateness of the integrated data. Be-
side the common webbased user interface (
http://agbi.techfak.uni-bielefeld.de/DAWISMD/
)
there is a
visualization component that allows interactive graphical exploration of the integrated data. However,
the data from the CardioVINEdb system have been proven useful to be analyzed on a large scale and
visualized in a biologically meaningful way for the quorum sensing system as well. An important aspect
