SysMO-DB: Supporting Data Access and Integration

SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The goal pursued by SysMO is to record and describe the dynamic molecular processes occurring in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. The aim is to pool research capacities and know-how from eleven projects. To facilitate this process, the Data Management Group (DMG) has been created to support data access and integration. Each of the individual projects in SysMO are working towards different research outcomes and represent a cross-section of microorganisms, including bacteria, archaea and yeast. The environmental conditions for each organism also vary widely with organisms growing in culture, soil, water and animal hosts. As a consequence of this diversity, there is no one model for experimentation or for the types of data collected and the types of models produced. In order to pool the research outcomes for SysMO, our job is to support and manage this diversity and promote a shared understanding across the community by using the same technologies. The underlying premises are (i) the systematic management of data, models and processes; (ii) the gathering of minimal information to support reproducible science, and (iii) shared best practice. The main objectives of a data management solution for SysMO are thus to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. The aim of this proposal is to present a progressive and scalable solution to the data management needs of the SysMO initiative, that: facilitates and maximises the potential for data exchange between SysMO research groups, maximises the 'shelf life' and utility of data generated by SysMO, provides an integrated platform for the dissemination of the results of the SysMO projects to the scientific community, and facilitates standardization of practices in Systems Biology for the interfacing of modelling and experimentation. We will adopt a progressive solution to the data exchange, comparison and dissemination needs of the SysMO initiative combining elements to support data storage and annotation, model storage and annotation, and the definition of (common) processes using workflows combining access to SysMO and external resources and for building models. We will provide unified access through a portal - the SysMO-HUB. We will create a catalogue of data assets - SysMO-SEEK; of models using JWS Online; and of workflows using myExperiment, and integrated search across all these through the HUB. We will help the partners develop their data management systemsand adopt community solution;, annotate models and adopt community standards and develop and share workflows using a de facto community system, Taverna. Metadata for discovery and exchange will be identified and developed on an on-demand basis sufficient without being overbearing. We will create an environment where the SysMO groups will be able to exchange their results as and when they want, disseminate their results outside the consortium and effectively use the resources of the wider Systems Biology community.

We will adopt a progressive solution, with regular staged delivery of capability, to the data exchange, comparison and dissemination needs of the SysMO initiative. The solution combines elements to support data storage and annotation, model storage and annotation, and the definition of (common) processes using workflows. There will be an emphasis on training, dissemination of best practice and 'help yourself' throughout the consortium in order to ensure sustainability and scalability. We will provide unified access through a secure portal - the SysMO-HUB - implemented using the Liferay Portal Framework, with fully customised access control. We will create a new, annotated, catalogue of data assets - SysMO-SEEK; of models using the JWS Online repository and simulator; and of workflows using the myExperiment workflow repository and social network system. Integrated search across all three repositories will be possible from the portal. Plugins through portlets will enable query and updates to datasets, model simulation and workflow execution. We will help the partners to: develop their data management systems and adopt where relevant community solutions such as SABIO-RK; accurately annotate models and adopt community standards such as SBML and MIRIAM; and develop and share workflows for the automated build of SBML models and the integration of resources within and without SysMO, using a de facto bio-community system, Taverna. Metadata for discovery and exchange of data, models and workflows will be identified and developed on an on-demand basis sufficient without being overbearing. We will create an environment where the SysMO groups will be able to exchange their results as and when they want to whom they want, disseminate their results outside the consortium and effectively reuse the resources of the wider Systems Biology community.