WPI: Project Management and Co-ordination Objectives The purpose of this work package is to manage and co-ordinate the preparatory phase in order to

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1 WPI: Project Management and Co-ordination The purpose of this work package is to manage and co-ordinate the preparatory phase in order to deliver the agreed objectives of this proposal. To manage the preparatory phase of the project. To establish and run the management structure (boards and committees). To establish and maintain a website for ISBE. To co-ordinate and deliver the preparatory phase activities on time and on budget. To coordinate activities of the ISBE project, guarantee a smooth flow of information, and to develop and manage reporting strategies among project partners and to the European Commission. WP2: Model and Data Management At the heart of ISBE is an infrastructure for the integration and synthesis of systems biology across the Data Generation, Integration and Stewardship Centres identified by the project. The distributed, interconnected infrastructure envisaged depends on the adoption of best practices, standards, technical infrastructure, software and capacity for data and model management and distribution. Model and data management covers technical, social and educational aspects. To comprehensively survey the state of the art and best practices for model and data management for Systems Biology in Europe. To propose and promote a framework and best practices for model and data management for Systems Biology in Europe. To collaborate with standardisation activities for model and data management WP3: Overall Infrastructure, Eligibility and Accessibility WP3 defines the central infrastructure of ISBE in terms of different types of dedicated research centres and the protocols for access to the ISBE centres. The specific objectives are: define the ISBE infrastructure define eligibility criteria to become part of ISBE infrastructure develop protocols for access to the ISBE infrastructure WP4: Data Generation Systems approaches require the collection, integration and storage of large data sets from genomics, proteomics, metabolomics and other omic fields as well as molecular imaging with the goal to model life processes. The aim of the Data Generation work package (WP4) is to develop the appropriate institutional infrastructure and scientific mentality to support the collection of high throughput quantitative data in the biomedical and biotechnology fields in a way that is fit for systems biology. The overall objective of WP4 is to translate the strategic vision developed in WP7 (Overall Infrastructure, Eligibility and Accessibility) into an infrastructure plan for the construction phase of ISBE. To document the existing physical infrastructures providing high throughput data generation of partner institutes in order to identify those that are relevant to ISBE. To develop a long-term, strategic vision of the role of high throughput data generation centres for systems biology research; To develop a distributed infrastructure prioritised plan to renovate existing infrastructures and build new infrastructures. To determine their contribution and impact on ISBE by constructing a roadmap of integrating relevant

2 proposals for national and pan-european construction plans. To design and define standards and harmonise procedures in the operation and management of the data generation centres and to ensure implementation of harmonised and standardised operating practices among users. To define the needs of the European scientific community regarding access to the Data Generation Centres. To develop a plan for the implementation of European access and to develop the strategies that will establish the rules for providing European access to the Data Generation Centres of ISBE. To assess the needs, survey existing solutions and define the future strategy for developing a distributed data storage infrastructure for systems biology that can efficiently cope with unprecedented data volume and will be linked closely to the data generation centres and modelling hubs of ISBE (in cooperation with WP3). WP5: Community Building and Synergies This WP is focused on identifying and engaging with all European stakeholders of the following categories: (a) researchers who already see themselves as systems biologists (including European research consortia), (b) those who do not, but could benefit from the ISBE infrastructure, (c) the broader groups of stakeholders: clinical researchers, industry, the media, policy makers, funding organisations and the general public at large, and (d) existing and emerging ESFRI projects in the field of Biological and Medical Sciences. One of the general goals will therefore be to identify a coherent view on the various needs of the different categories of stakeholder, including additional technology applications especially in the fields of Bioinformatics, Bioimaging, Chemical Biology and Synthetic Biology. The work can be divided into the following broad objectives: Identifying the systems biology community and assessing the broader understanding of systems biology by multiple stakeholder groups. Providing a central portal for access to all general information, and as a means for dialogue/communication within the community. Gathering information of relevance to the community and co-ordinating the sharing of expertise. Surveying international research infrastructures and successful infrastructure networks outside of ESFRI and promoting ISBE partnership options Developing illustrative case studies for stakeholder groups and promoting ISBE to the European systems biology community Establishing a mechanism for on-going expansion of the Systems Biology community, especially into the extended European area (Eastern Europe etc.) Set-up a full debate on the possible development of a European systems biology society, especially for its potential value in lobbying funding agencies, national and European funding programmes (HORIZON2020) and regulatory bodies. Coordination and communication of ISBE preparatory phase with ongoing and emerging projects within the ESFRI roadmap and the area of Biological and Medical Sciences (BMS) i.e. scientific interfacing with bioinformatics screening and imaging as well as data resources, biobanks of European and leading international systems biology infrastructures Developing collaboration agreements with existing ESFRI initiatives and objectives for multi-esfri nodes (including agreements on accessibility and real-time connections between ISBE and other ESFRI projects).

3 WP7: Strategy, Vision and Advocacy The objective of the ISBE Preparatory Phase is to lay down a strategy, vision and advocacy pipeline for the implementation of the ISBE at a subsequent phase. This WP aims at developing an initial basis for the implementation plan and operation of a European infrastructure in Systems Biology, and to reach a community-supported consensus in mapping the needs, bottlenecks and potential of the various aspects of Systems Biology in a broad range of areas. WP8: Modelling Infrastructure and Expertise Provide the scientific and organisational foundation for a rapid and highly coordinated pan-european implementation of an extensive modelling service for academia and industry across all major disciplinary fields of biology through: provision of showcases documenting the importance of modelling identification of key resources for a pan-european modelling service obtaining a pan-european consensus on how to organise a modelling service WP9: Technology and Science Watch During the preparatory phase the infrastructure needs to get an estimate of the state of the art with respect to existing and emerging technologies to formulate a technology vision for the operational phase of the infrastructure before starting its actual operation. One example that might be mentioned is the importance of new phenotyping technologies. Additionally, a systems needs to be established that ensures the continuous assessment of new scientific and technology areas in a standard way. For that a technology and science assessment council should be established, and mechanism need to be defined and established by which the council operates (surveys, meetings, focused workshops) Formulation of a technology vision for the operational phase of the infrastructure Define and establish procedures for the continuous assessment of emerging technologies relevant to ISBE. Taking actions to implement new innovative technologies and procedures to ISBE s technology tools and research topics Identification of the future needs of the systems biology community with respect to storage and hardware. WP10: Training and Education This WP addresses education and training. The need for scientists specially trained in systems biology is now widely recognised. An important aspect of the work under this work package will be to carry out an audit of existing programmes and courses, from the point of view of applicability to the ISBE and best practice. It is envisaged that this will result in detailed recommendations relating to interdisciplinary programme planning and course content. To identify ISBE training centres and best practice in current systems biology education at the graduate and post-graduate levels in Europe and beyond. To network and support ISBE training activities and to create a web-based tool for disseminating information related to ISBE training and best practice. To review ISBE curricula in systems biology and to define a core curriculum, plus sector based options.

4 To create a pilot multicentre EU programme in systems biology WP11: Funding, Governance and Legal In order to establish viable, long term, sustainable, funding and a legal framework for ISBE, it must build upon the strategic activities of European national funding agencies and engage with them in establishing support. The of Work Package 11 are:- To understand and document the challenges to be met to establish a pan- European infrastructure that capitalises on existing national and European funding for research and co-ordination in systems biology. To identify and document current funding mechanisms and instruments for co-ordination of resources across European ministries and funding organisations interested in ISBE. To map the scope and duration of different funding segments of the infrastructure, to enable their effective and efficient integration and operation, and to develop governance models against the mapping. To deliver an interim funding and governance phase, based on the mapping of funding segments and strategic priorities of funding organisations participating in ISBE. To recommend indicative funding requirements for the co-ordination and integration of the different segments of infrastructure. To deliver a long-term funding and governance strategy that supports the objectives and priorities of funding organisations participating in ISBE. To provide a business plan and mechanisms for negotiation of International Consortium Agreement, for the subsequent construction phase of ISBE, - to be reviewed and agreed by the Steering Committee WP13: Connections The Infrastructure for Systems Biology in Europe (ISBE) will consist of nodes (see WP3) and strong connections between these. Particularly Systems Biology needs to integrate various types of expertise that do not exist at a single location at the highest level of excellence. WP13 has the aim to make these connections seamless, ultrafast and user friendly. More specifically the objectives are: to define and design all possible connections between ISBE nodes that will promote European Systems Biology to design standard interfaces at ISBE nodes that enable computer assisted connecting to design ways in which large systems biology tasks can be partitioned over nodes and the results reintegrated WP15: Innovation, Impact and Exploitation Innovation, Impact and Exploitation are key drivers of systems biology for the major stakeholder groups encompassing (i) life sciences and clinical communities (ii) industry and (iii) society. Investing and encouraging innovation by use of systems biology infrastructures will be a priority in Europe, as well as measuring its impact offset by sustainability. A third element linked to innovation and impact will be exploitation, in which we assess the affordability and quality delivered through the ISBE in conjunction with existing work packages including WP2 (Model and Data Management), WP3 (Overall Infrastructure, Eligibility and Accessibility), WP5 (Community Building and Synergies), WP7 (Strategy, Vision and Advocacy), WP9 (Technology and Science Watch) and WP11 (Funding Governance and Legal).

5 This work package will survey and explore major elements and mechanisms: that underpin new models of Systems Biology research in basic and applied sciences that enable innovative approaches in health and life sciences in or between academia and industry that improve efficiency to transfer laboratory findings to treatments in medicine agri-food and life-sciences in general that ensure exploitation and management of intellectual property in ISBE collaborations that promote existing structures and identify new models for commercialisation that explore the impact of existing policy on the sustainability, affordability and quality of the systems biology pipeline to exploitation

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