|
|
|
|
| |
|
|
| Rasanpreet Kaur; Anwesha Dutta; Martina Kutmon; Martijn Iersel; Chris Evelo. |
| Biological molecules such as proteins and metabolites interact to accomplish a biological function and to respond to environmental stimuli. Pathways capture this information derived through scientific experimentation and data analysis. They contain information about genes that appear in complexes, the interacting genes, the directionality of the interactions (e.g. inhibitors versus activators), the cellular locations where the reactions occur, and the metabolites that are affected by the processes. Using our open-source pathway analysis platform, PathVisio, we will connect pathway analysis to different quantitative approaches already in development for metabolic network modeling, such as flux balance analysis and dynamic simulation. In order to use... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6970/version/1 |
| |
|
|
| Martina Kutmon; Martijn P. van Iersel; Thomas Kelder; Chris T. Evelo. |
| In the last decade the amount of Bioinformatics tools has increased enormously. There are tools to store, analyse, visualize, edit or generate biological data and there are still more in development. Still, the demand for increased functionality in a single piece of software must be balanced by the need for modularity to keep the software maintainable. In complex systems, the conflicting demands of features and maintainability are often solved by plug-in systems.

For example Cytoscape, an open source platform for Complex-Network Analysis and Visualization, is using a plug-in system to allow the extension of the application without changing the core. This not only allows the integration of new functionality... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6113/version/1 |
| |
|
|
| Martina Kutmon; Nicolas Rodriguez. |
| The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. Recently a prototype has been developed with OSGi to achieve a more modular framework structure. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules. SBFC allows anyone to easily add new... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6370/version/1 |
| |
|
|
|
