Info

Experimental Data

Objective: Establish platforms for sustainable (meta)data storage and traceable data analysis

Rationale

Biomedical research generates a continuous flow of molecular profiling data. In many cases, such data is generated in the context of one particular study, while being of value to other studies. However, data and the specifics of the experiments (metadata) frequently get lost once a study is finished. To prevent this, data should be stored in a findable, accessible, interoperable, and re-usable manner.

To enable re-use of data and traceable data analysis, TraIT WP4 offers molecular profiling platforms for sustainable (meta)data storage and (bioinformatics) analysis focusing on four technology domains:

- DNA and RNA Next Generation Sequencing (NGS)

- DNA and mRNA microarrays

- Mass spectrometry-based proteomics

- Non-omics laboratory assays such as PCR, IHC, etc.

 

Target groups

- Biomedical researchers ('wet-lab')

- Bioinformaticians ('dry-lab')

 

Approach

Because of the differences between the four technology domains, each domain is approached separately. Pilot projects focused on selecting the most suitable generic solutions and development of specific applications or connections where needed. For each technology domain a platform and pipeline will be set up that generates processed data, which allows seamless integration with TraIT tranSMART WP5 Core Infrastructure.

  • NGS: DNAseq and RNAseq, using TraIT Galaxy
  • Arrays: arrayCGH and mRNA arrays, using Chipster
  • Proteomics: Tandem mass spectrometry (MS) and targeted MS, using colims
  • Non-omics: non-high throughput laboratory assays, using Phenotype database

 

Status

- Deployment of Chipster has been realized and the tool is available.

- Deployment procedures for Galaxy and Phenotype Database are ongoing and these tools will soon become available.

- colims developed by and accessible via the Computational Omics and Systems Biology Group of Lennart Martens at the University of Ghent.

 

More information

Work Package leader: Remond Fijneman (VUmc)

r.fijneman <at> nki.nl