WP3

Overall infrastructure, eligibility and accessibility

WP3 defines the central infrastructure of ISBE in terms of the three types of easily accessible ISBE expertise centres.

Objectives of WP3 are:

  • define the ISBE expertise
  • develop protocols for easy client access to the ISBE centres and their expertise
  • formulate eligibility criteria to become an ISBE expertise centre

 

The core of the ISBE infrastructure is a matrix of functionally interconnected ISBE expertise centres throughout Europe. It gives access to expertise in model-driven approaches in the life sciences, i.e. systems biology. ISBE covers the complete systems biology workflow, including:

  • planning of the project (experimental design), including access to already existing data sets, maps and models
  • generation of standardised experimental data sets that are fit for modelling
  • annotation, curation and making accessible of systems biology relevant and standardised data, models, simulations, maps and tools
  • develop community-based standards in experimentation and data acquisition that allow re-use in other projects
  • development, analysis, validation and use of predictive and quantitative models aiming at in-depth integrative understanding of biological systems

 

Described below are our current idea’s about the ISBE Infrastructure. More information about the centres can be found by visiting Expertise Centres.

Modelling and Integration Centres (MICs)

  • planning (experimental design)
  • workflows of planning, data acquisition and modelling
  • mathematical modelling of a wide range of different biological systems in different application frameworks
  • standardisation of experiments, data sets and models
  • allow re-use of data, models, maps, etc.
  • support clients in model-based simulation
  • integration of diverse types of experimental data, theory and other information
  • parameter estimation, parameter sensitivity analysis, uncertainty analysis, model validation, etc.

 Data Generation Centres (DGC)

  • expertise, equipment and personnel for the acquisition of high-, medium- and low throughput data sets that are tuned to model building
  • advice in the experimental design phase about data storage and data analysis
  • carry out data generation tasks
  • contribute to the development and implementation of SOPs
  • develop user-specified applications (methodology development)

Stewardship Centres (SC)

  • contribute to developing and agreeing on community standards and formats for exchanging data and models
  • contribute to the standardisation of formats, ontologies and minimum information checklists; linking of data to models, SOPs and experimental descriptions
  • digital curation of data, models, experimental protocols, maps and tools
  • transforming relevant existing data sets to formats that can be used in
  • systems biology projects
  • digital preservation or migration of ISBE-related data, models and maps to
  • established archives and repositories
  • recommendations for tools and resources to assist with standards compliance,
  • lower the barrier to adoption and to make standards-compliance more efficient and less time-consuming

 

Work Package Leader Roel van Driel UvA
Project Officer (contact) Frans van Nieuwpoort UvA
Partners Dimitris Thanos BRFAA
Richard Kitney IC
Jutta Steinkoetter MDC
Kristina Gruden NIB
Hans Westerhoff VUA
Angela Oberthuer UHEI
Stefan Hohmann UGOT
Vitor Martins dos Santos WU-ATV
Stig Omholt UMB
Carole Goble UNIMAN
Garry Corthals CBT