High-throughput sequencing assays are now routinely used to study different aspects of genome organization. As decreasing costs and widespread availability of sequencing enable more laboratories to use sequencing assays in their research projects, the number of samples and replicates in these experiments can quickly grow to several dozens of samples and thus require standardized annotation, storage and management of preprocessing steps. As a part of the STATegra project, we have developed an Experiment Management System (EMS) for high throughput omics data that supports different types of sequencing-based assays such as RNA-seq, ChIP-seq, Methyl-seq, etc, as well as proteomics and metabolomics data. The STATegra EMS provides metadata annotation of experimental design, samples and processing pipelines, as well as storage of different types of data files, from raw data to ready-to-use measurements. The system has been developed to provide research laboratories with a freely-available, integrated system that offers a simple and effective way for experiment annotation and tracking of analysis procedures.
|Original language||English (US)|
|Journal||BMC systems biology|
|State||Published - 2014|
Bibliographical noteFunding Information:
The authors thank Ali Mortazavi for critical discussion of the manuscript. This work has been funded by the STATegra project, EU FP7 grant number 30600. This work was partially supported by COST-BMBS, Action BM1006 “Next Generation Sequencing Data Analysis Network”, SeqAhead. The contribution of IA was also supported by Åke Wibergs Stiftelsen medicine research Diarienr: 719593091 (http://ake-wiberg.se/).
ASJC Scopus subject areas
- Structural Biology
- Modeling and Simulation
- Molecular Biology
- Computer Science Applications
- Applied Mathematics