Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools and Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract VANESA (Visualization and Analysis of NEtworks in Systems Biology Applications) is a software solution that can be used to visualize and examine networks in systems biology applications.

It addresses biomedical case studies and has been used to create and model individual network systems and their detail information.

VANESA, a new editor-controlled information system provides new bioinformatics methods and visualization approaches to analyze dynamic interacting networks.

The idea of VANESA is to extend any molecular data based network by new targets and interacting elements.

The main aim(s) of VANESA is to provide scientists with advanced features (see below...) to examine some of the essential questions in natural science.

Aims of VANESA --

Biological networks have always been of wide interest. Over many years of research, activities took place on biological phenomena with the motivation to discover some of their secrets.

Over time, natural science and its studies on living organisms have answered many essential questions. But still, a lot of biochemical processes are far beyond our understanding.

During the research process enormous amounts of biological data are produced. Information from different fields of studies are brought together in order to examine and analyze quantities and relationships.

The accurate representation of data is one of the main tasks in computer science. Information must be visualized in a clear and understandable manner to meet the purposes of the underlying research activities.

The aim of VANESA is to address the above points. VANESA’s software framework gives the biological scientist the opportunity to characterize a biological system with all its relevant details in order to reach the overall goal of a sophisticated representation.

The approach of extracting, analyzing and modeling meaningful biological data of heterogeneous data sets as a biological network is one of the big strengths of this software application. And with the features of VANESA, biological scientists can get a step closer to the answers they are looking for.

VANESA features/capabilities include:

1) Modeling and editing of biomedical networks -

2) Consulting biomedical databases -

VANESA is built upon the CardioVINEdb data warehouse, which provides some of the most important life science databases, such as UniProt, KEGG, OMIM, Gene Ontology (GO), ENZYME, BRENDA, PDB, MINT, SCOP, EMBL-Bank, and Pub-Chem.

The CardioVINEdb data warehouse was exclusively constructed for the EU project CardioWorkBench. Currently, the CardioVINEdb data is integrated into the Data Warehouse Information System for Metabolic Data (DAWIS-M.D.).

DAWIS-M.D. is a platform independent 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-datedness of the integrated data.

Besides the common web-based user interface there is a visualization component that allows interactive graphical exploration of the integrated data.

An important aspect of visualization is the consideration of multi-dimensional data annotations in a way suitable for the information discovery process.

3) Analysis -

Furthermore, the above mentioned data sources provide an established basis for the modeling and characterization of a biomedical system. The data integration is an advanced feature of VANESA that provides many possibilities.

VANESA's graph comparison and graph theory functions support the user in a better understanding of biological circumstances. Highlighting and comparison functions point out important facts in a set of different models.

In order to make the graphical representation and the analysis on the networks more legible, graph layout transformations and animation algorithms are considered as well.

Another important feature of VANESA (as stated above...) is that information is visualized in a clear and understandable manner to meet the purposes of underlying research activities.

With an intuitive graphical user interface, the user is enabled to record research results and thoughts in the form of a ‘digital network’ model.

The user is Not limited to any kind of biological model; moreover it is possible to create an individual system that meets the requirements of each research activity.

For additional info and a case study application of VANESA refer to:

S. Janowski, B. Kormeier, T. Töpel, K. Hippe, R. Hofestädt, N. Willassen, R. Friesen, S. Rubert, D. Borck, P. Haugen and M. Chen; Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing; In Silico Biology 10, 0003 (2010).

System Requirements

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Manufacturer Web Site VANESA

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G6G Abstract Number 20618

G6G Manufacturer Number 104219