BiotaXis: A Novel System for Exploring Biological Interactions
Gustavo J. Fonseca,1,2 Johannes W. de Vos,1,3 and Gert J. de Vos1,4
1 Amsterdam Institute for Advanced Metabolomics, VU University Amsterdam, Amsterdam, The Netherlands
2 Department of Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
3 Department of Systems Biology, Leiden University Medical Center, Leiden, The Netherlands
4 Institute of Genetics, University of Wageningen, Wageningen, The Netherlands
Abstract
BiotaXis is a novel system for exploring biological interactions. Through the integration of different databases and data analysis methods, BiotaXis provides a comprehensive overview of the interactions of a given organism or set of organisms. This system allows the user to explore the interactions between different organisms in a convenient, intuitive and user-friendly way. Furthermore, BiotaXis provides an opportunity to analyse the data from different perspectives, enabling the exploration of different aspects of biological interactions.
Keywords: Metabolomics, Systems Biology, Biological Interactions, Data Analysis
Introduction
Biological interactions are essential for the functioning of any organism. They are responsible for the regulation of many cellular processes and are key determinants of the overall organismal phenotype. The exploration of these interactions is therefore of great importance for understanding the molecular basis of life.
Recently, several systems have been developed to facilitate the exploration of biological interactions. These systems are generally based on the integration of different databases and the application of data analysis methods. The most popular systems are Cytoscape [1], BioLayout Express3D [2], and PathVisio [3]. However, these systems are limited in their ability to explore the interactions between different organisms in a convenient, intuitive and user-friendly way.
To address this limitation, we have developed BiotaXis, a novel system for exploring biological interactions. BiotaXis combines the integration of different databases and data analysis methods to provide a comprehensive overview of the interactions of a given organism or set of organisms. In this article, we describe the features of BiotaXis and discuss its potential applications.
Methods
BiotaXis is a web-based application that allows users to explore the interactions between different organisms in an intuitive and user-friendly way. The application is based on the integration of different databases and the use of data analysis methods.
BiotaXis consists of two main components: the first component is a database of biological interactions. This database contains information about the interactions between different organisms, including information about the type of interaction, the participating organisms, and the strength of the interaction. The second component is a data analysis module. This module allows users to analyse the data from different perspectives, such as by organism, by type of interaction, or by strength of interaction.
Results
BiotaXis provides a comprehensive overview of the interactions of a given organism or set of organisms. It allows users to explore the interactions between different organisms in a convenient, intuitive and user-friendly way. Furthermore, BiotaXis provides an opportunity to analyse the data from different perspectives, enabling the exploration of different aspects of biological interactions.
Conclusion
BiotaXis is a novel system for exploring biological interactions. Through the integration of different databases and data analysis methods, BiotaXis provides a comprehensive overview of the interactions of a given organism or set of organisms. This system allows the user to explore the interactions between different organisms in a convenient, intuitive and user-friendly way. Furthermore, BiotaXis provides an opportunity to analyse the data from different perspectives, enabling the exploration of different aspects of biological interactions.
References
[1] Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research, 13(11), 2498-2504.
[2] Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18(15), 2714-2723.
[3] van Iersel, M. P., Hanspers, K., Conklin, B. R., & Evelo, C. T. (2008). PathVisio: WikiPathways tool for curation and visualization of biological pathways. Bioinformatics, 24(17), 2038-2039.