ISBE An infrastructure for European (systems) biology Martijn J. Moné Seqahead meeting “ICT needs and challenges for Big Data in the Life Sciences” Pula, Italy | June 6, 2013

Background Rationale The amount of detailed data and information on components of living systems continues to increase But our ability to understand dynamic interactions within systems remains a challenge It has not been possible to tackle these challenges effectively because of: Technical limitations Limited access to a small number of specialist groups

The Opportunity Rationale This situation is now rapidly changing So, it is now timely to develop an infrastructure to coordinate the distributed European research effort in Systems Biology

Why now? Rationale High-speed DNA sequencing NGS Powerful computers Broadband networks The Internet The influence of engineering, physical science, computer science, mathematics

ISBE Rationale Will enable researchers to address how the interaction of biological components leads to the functioning of living organisms in constantly changing environments Create models of living organisms at various scales representing these interactions Exploit this information to generate major socio-economic benefits in areas including health, agriculture, environment

ISBE The Facility Objective 1 Interconnect hubs of technological excellence in systems siology through offering the best in European research expertise, and experimental and modelling facilities, necessary for systems biology Objective 2 Establish and make available repositories of data and models Objective 3 Enable (real-time) connections within and between components 1 and 2 and with external user laboratories This will be done as much as possible through the provision of high performance connections to existing high capacity network infrastructures

ISBE The Facility

Centres (or Nodes / Hubs) The Facility Hubs will contribute specific skills and expertise to functional clusters focussed on a variety in an operational matrix Some Hubs may have groups that participate in different and/or multiple clusters

Facilitate Interaction The Facility The aim will be to facilitate efficient interaction with the substantial technology development efforts (relevant to systems biology) already funded by national and EU programmes ISBE will enable all European laboratories to model and conduct experiments and undertake essential activities remotely – where they cannot be done locally

Status of the Project Status The 3-yr Preparatory Phase started in Aug 2012 The work packages include: Project management and co-ordination Model and data management Overall infrastructure, eligibility and accessibility Data generation Community building and synergies Strategy, vision and advocacy Modelling infrastructure and expertise Technology and science watch Training and education Funding, governance and legal Connections Innovation, impact and exploitation

Challenges Complexity of the project Interface between WPs Interfacing with other research infrastructures Engagement with stakeholders

Challenges Connecting the nodes Data generation: High throughput of imaging/anatomical information Integration of other levels of information into molecular models Standards, SOPs Data analysis/stewardship: Automation of data analysis Training for non-bioinformaticians Data integration/modeling: Toolbox for non-SBists, model repository Model building, coupling of scales (temporal, spatial) Support for planning and generation of appropriate data

Challenges Connecting all the nodes to define and design all possible connections between ISBE nodes that will promote European systems biology to design interfaces among all 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

Single point of entry/exit DGCs DIC DSCs DGCs e.g. ELIXIR Modelling-centric

ISBE nodes and connections Connections – Nodes (or node collectives) Generation Stewardship Integration

ISBE nodes and connections Reinforcement by output OUTPUT

Data integration vision Connecting data, models and expertise ISBE as the driver of (a) visionary project(s) with great scientific and societal impact. ISBE + main driver would serve – and transform – life sciences. Virtual maize, virtual yeast, virtual human Can draw from the same resources Human Virtual human OrgansDiseaseNutrition….other Plant Model PlantsCrop Plants Plant- pathogen interaction …other Microbe Model organisms PathogensBiodiversity…other Animal Model organisms Farm Animals …other Interaction EnvionmentDiseasesEcology…other …other topics …other

Thank you! See us at ICSB 2013 – Copenhagen 30/8 - 3/9 Martijn Moné, Hans Westerhoff VU University Amsterdam