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

ISBEAn infrastructure for European (systems) biologyMartijn J. MonéSeqahead meeting “ICT needs and challenges for Big Data in the Life Sciences” Pula, Italy | June 6, 2013

BackgroundRationale

• 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 OpportunityRationale

• 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

ISBERationale

• 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

ISBEThe 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

ISBEThe 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 InteractionThe 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 ProjectStatus

• 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

ChallengesConnecting 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

ChallengesConnecting 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

DSCsDGCs

e.g.ELIXIR

Modelling-centric

ISBE nodes and connectionsConnections – Nodes (or node collectives)

GenerationGeneration

Generation

Stewardship

Inte

grati

on

ISBE nodes and connectionsReinforcement by output

OU

TPU

T

Data integration visionConnecting 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

Thank you!

See us at ICSB 2013 – Copenhagen 30/8 - 3/9

Martijn Moné, Hans WesterhoffVU University Amsterdam