March 3, 2017

Sixth abstract for Eagle Symposium 2013

Following in the series of abstracts from the last few weeks, this week we share with you Katy Wolstencroft's abstract. Katy is from the University of Manchester. The presentation title is: "Sharing Data, Models and Procedures between Systems Biologists: Technical and Social Engineering"

Abstract: Systems Biology aims to integrate biological knowledge and data in order to model and predict the function of whole biological systems. Research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. With a Systems approach, mathematical models are developed iteratively from data generated in the laboratories, from public repositories and the literature. Some of this data includes large, high throughput experiments, such as Next Generation Sequencing, but some includes relatively small, quantitative data sets. As a result, research in this discipline may experience problems associated with large data, but a more common problem is access to the many different types of data required. While there are public repositories for sequence and expression data, repositories for metabolomics data, for example, are lacking. In addition, submitting data to these 'silos' means that relationships between data sets, and between data and models can be lost.

The SEEK is an open-source, web-based platform for the management and exchange of Systems Biology data, models and experimental protocols. It enables scientists to share data and models in the context of the experiments that created them, recording and describing the connections between data and models. Access to individual datasets and models is controlled by the scientists uploading them, so the SEEK functions as both a private consortium sharing environment and a platform for public dissemination. The SEEK was originally developed for the SysMO consortia (Systems Biology of Micro-Organisms), but the principles and objectives are applicable to any Systems Biology project, and it has since been adopted by a number of other consortia.

The SEEK is a pragmatic solution to data management which encourages, but does not force, researchers to share and disseminate their data in community standard formats. It builds on available community metadata standards by providing software to embed standards-compliance into tools already in common use (such as spreadsheets), and provides incentives and added value for following SEEK metadata recommendations.

With the help of a group of early career experimentalists and modellers from the SysMO projects - the SysMO PALs - we have designed a system that promotes the annotation, exchange and reuse of Systems Biology resources whilst hiding some of the complexities of data and metadata management from users.

Topics: Bioinformatics, life science event, symposium 2013, Will big data and bigger cuts cripple bioinformati