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| Chris T. Evelo. |
| Biology is rapidly developing into a data-driven science and faces not only the challenge of coping with an ever growing amount of data but also that of interpreting its complex diversity. The requirement of systems biology to connect different levels of biological research leads directly to a need for large scale data integration. The nutritional phenotype database (dbNP) addresses this challenge for nutrigenomics. A particularly urgent objective in coping with the data avalanche is making biologically meaningful information accessible to the researcher. In this presentation we will describe how we intend to meet this objective with the nutritional phenotype database. We will outline relevant parts of the system architecture, describe the kinds of data to... |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5141/version/1 |
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| 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 |
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| Andra Waagmeester; Helena Deus; Chris T. Evelo. |
| Biology has become a data intensive science. Discovery of new biological facts increasingly relies on the ability to find and match appropriate biological data. For instance for functional annotation of genes of interest or for identification of pathways affected by over-expressed genes. Functional and pathway information about genes and proteins is typically distributed over a variety of databases and the literature.

Pathways are a convenient, easy to interpret way to describe known biological interactions. WikiPathways provides community curated pathways. WikiPathways users integrate their knowledge with facts from the literature and biological databases. The curated pathway is then reviewed and possibly corrected or... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6679/version/1 |
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| Chris T. Evelo. |
| Until recently nutrigenomics was mainly about transcriptomics related data. That already confronted us with overwhelming analytical problems. We learned to mathematically and statistically treat genome wide expression studies and studies directed to gene expression regulation. Nutrigenomics researchers had to become bilingual speaking: English and R1 and learned to think about co-expression, clusters and false discovery rates. The latter in fact proofed to be a trap. Removing all the false positives made us loose the information we were really interested in. To understand the results of our genomics experiments we often had to confront what we were measuring with what we already knew. After all false positives are not likely to all be related to the same... |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5689/version/1 |
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