A new and improved version of the Phenotype database is available. The main changes compared to V1 are:

  • New User Interface
  • Introduced a timeline to the “Design” part, to simplify study design
  • New importer with many performance improvements
  • Many fixes to the analyses/visualization functionality
  • Improvement of displaying large amounts of data
  • Updated short and extended manual

Click here for the source code

Click here for the short manual

Click here for the extended manual

The Clean Transcriptomics Database is a module of the Nutritional Phenotype Database (dbNP). The development of this module is funded by NuGO and built by Wageningen University & Research Centre. It aims at a centralized storage of transcriptomics data, that is queryable via the dbNP query module, and has its accompanying study metadata stored in the dbNP study capture module (GSCF, see under).

It complies with the ‘dbNP omics submodule’ standard by serving clean data via the dbNP clean data layer.

Click here for source code

License

Apache 2.0

The metagenomics module, attached to GSCF, stores genetic sequencing data derived from environmental samples, such as bacteria.

The metagenomics module is developed in the ANTIRESDEV project, which receives funding from EU FP7. Among others, its aim is to gain knowledge of the dynamics of resistance emergence at a variety of body sites during the administration of a range of antibiotics frequently used in Europe.

Click here for source code

Click here for poster

License

Apache 2.0

The metabolomics module functions as a repository of metabolomics data, facilitating storage of raw and processed metabolomics data and study information, which can be searched and queried.

This module is part of the NMC DSP, a data support platform for metabolomics studies built by Netherlands Metabolomics Centre (NMC), to support storage of experimental metabolomics data, and their processing. This bioinformatics support platform will provide a means for communication between the partners of the NMC for the exchange of data, software, and tools. (See also our portfolio.)

Click here for source code

Click here for the Metabolomics User Guide (PDF)

License

t.b.d.

The Nutritional Phenotype project (dbNP) is an open source ecosystem for multi-omics databases. One of the modules of dbNP is the Simple assay module (SAM), in which it is easy to import bulk numerical data from e.g. Excel files. It is used to store clinical data, such as Rules Based Medicine assays, but also physical measurements such as body weight of mice. Continue reading