SysMO-DB2

Systems biology is a biology-based inter-disciplinary study field combining experimental investigations and computational modeling to discover emergent properties of complex interactions in biological systems. SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The initiative's goal is to record and describe the dynamic molecular processes that occur in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. Each project is made up of a consortium of European institutions and each works towards different research outcomes on a variety of microorganisms, including bacteria, archaea (single-celled microorganisms) and yeast. The environmental conditions for each organism vary, growing in culture, soil, water and animal hosts. This diversity means that there are many different kinds of models and many different types of data collected. The SysMO initiative has been divided into two phases: SysMO1 funded eleven projects and 91 institutions; SysMO2 will fund seven projects, five of which are project continuations from phase 2 (so six projects are concluded) and two of which are new. The research outcomes (models, data, procedures), and the know-how and best practice developed by the scientists, are to be managed and pooled in order to: benefit the members of the programme during the running of the projects; disseminate and publish the results to the wider scientific community; and safeguard the results after the completion of the projects that maximises the 'shelf life' and utility of data generated by SysMO. SysMO-DB is a project to build and manage an incrementally developed web-based software platform to achieve this. SysMO-DB1, funded during the first phase, begun the development of a web-based platform - called the SEEK - for cataloguing the different outcomes of the projects, archiving data, procedures and models and integrating with the different project's local data management systems, including the standardisation of the information used to describe the data and models and the handling of project spreadsheets. The SEEK also includes a social network for the SysMO members and integrates with public repositories for data, models, analyses and publications such as JWS Online (for models); SABIO-RK (for data), myExperiment (for bioinformatics data analysis pipelines) and PubMed (for publications). SysMO-DB has also developed effective practices for working with SysMO scientists through the founding of a PALs focus group of researchers who shape the developments, data standards and protocols necessary for pooling and promote SEEK adoption in their own projects. The focus of SysMO-DB1 is on supporting the current projects. SysMO-DB2 continues and extends the work to cope with SysMO-phase changes and life after beyond and after SysMO: new and terminating projects, personnel change, publication outside the consortium and long-term preservation of results. SysMO-DB2 also plans to package up the software and methods so that they can be adopted and sustained by other programmes such as EraSysBio+. EraSysBio+ is a pan-European programme for 16 Systems Biology projects. It is similar in organisation to SysMO but radically different in terms of scope. Hence it differs in the data, model and process capabilities needed. As part of widening the adoption of the SysMO-DB approach the project will support EraSysBio+ in its first 18 months. The two projects from EraSysBio+ that focus on microorganisms will be fully integrated into the SysMO-DB work programme. For the full range of EraSysBio+ projects SysMO-DB2 will instantiate a new instance of the SEEK, provide advice and help launch a PALs scheme.

SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The initiative's goal is to record and describe the dynamic molecular processes that occur in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. Each project is made up of a consortium of European institutions and each works towards different research outcomes on a variety of microorganisms under a variety of conditions leading to different kinds of models and different types of data collected. Phase 1, SysMO1, funded 11 projects. In phase 2, SysMO2 funds 7 projects, 5 continuations (6 projects are terminated) and 2 new. The SysMO-DB project aims to create and deploy a lightweight, technical infrastructure in order to: (i) pool the SysMO research capacities and its members' know-how, (ii) enable dissemination of results within and between projects, between participants, and to the scientific community, and (iii) support SysMO researchers in their routine work to manage their data, models and processes. SysMO-DB, addresses challenges in 5 areas: (i) developing and releasing the SysMO-DB SEEK software platform; (ii) managing the SEEK service; (iii) defining data exchange models, controlled vocabularies and curating models; (iv) establishing a strong user community engagement through a focus group of PALS; and (v) promoting adoption and sustaining the SEEK software, service and community. SysMO-DB2 extends the work to cope with new and terminating projects changes, long-term preservation and life beyond and after SysMO. SysMO-DB2 will package up the software and methods to be adoptable by other programmes such as EraSysBio+, pan-European programme for 16 Systems Biology projects. SysMO-DB2 will instantiate an EraSysBio+ instance of the SEEK, provide advice and help launch a PALs scheme. Two micro-organism projects will be fully integrated into the SysMO-DB.

SysMO-DB is about rapidly, retrospectively and sensitively creating and deploying a lightweight, technical infrastructure in order to: (i) pool the SysMO research capacities and its members' know-how, (ii) enable a seamless dissemination of results within and between projects, between participants of the model-hypothesis-experiment-model systems biology cycle, and to the scientific community, (iii) support SysMO researchers in their routine work to manage their data, models and SOPs and the data, models and SOPs relevant to their work. Currently SysMO-DB is an inward-looking, gated community. By the end of SysMO2 must be outward-looking and open to wider membership and public access in order to make the greatest impact outside the bounds of the SysMO partners. The expected outcome is an information exchange system for Systems Biology in Europe that: (i) works and is adopted and used; (ii) matches the practical needs of experimentalists and modellers and helps them work together; (iii) has a network of people who know how to use it and who spread the word about it; and (iv) is adopted by other programmes and communities. Thus the objectives of the proposal are targeted at ensuring, enabling and driving impact for many stakeholders: for the SysMO projects, for academic and industrial researchers outside the programme and for organisations and initiatives that need a similar information platform. Computer scientists will benefit from an opportunity to deploy Web 2.0 and Web 3.0 technologies in the field. The stakeholders will benefit in a number of ways. SysMO members will have a safe haven for their data, assistence and training in data and model metadata management, access to modern, labour-saviing bioinformatics technologies such as workflows, access to previously unrecognised resources and access to new techniques for data comparison, model validation etc. They will benefit from the visibility of, and access to, pooled assets and membership of a social network of researchers and their capabilities. This latter point could lead to new means of forming cooperations. The managers of public repositories will benefit from well curated assets that are suitably fit for deposition at the point of publication, and the SysMO members benefit from a new publication route. Managers and participants of similar intiatives will benefit from access to new technology and a new platform that they can deploy and adapt. Researchers outside SysMO will benefit from the secured results of SysMO. Thus the Systems Biology research community will benefit from advances in technology and knowledge for new avenues of work and collaboration. The proposal intrinsically incorporates a plan to ensure impact broadily categorised into these areas. - The platform itself for the exchange of SysMO outcomes during the initiative and the preservation of outcomes at each projects' completion - The development of the platform such that it can be readily sustained after the project ends, and readily extended and adopted by other initiatives - The PALS and programme of user engagement to ensure that the platform is fit for purpose and the SysMO community (and beyond) are capable of adopting it - A programme of dissemination of the SysMO-DB SEEK platform and the development of cooperations with key stakeholders such as the EMBL-EBI 'omics data resource managers.