Linking Data to Models

• Gather requirements for model management in SysMO-SEEK
• Work out common practices and determine “Just enough” for publishing and sharing in SysMO-SEEK

9:00 - 9:15 – Introduction to Workshop – Katy Wolstencroft sysmo-summary2.ppt

9:15 - 10:00 - Example workflow for modelling process – Jacky Snoep workflow.pdf

10:30 - 11:30 – Example of modelling processes from MCISB – Neil Swainston and Daniel Jameson informatics_in_the_manchester_centre_for_integrative_systems_biology.ppt

11:30 - 12:30 – Discussion about modelling processes

14:00 - 14:15 - SEEK progress - Stuart Owen seek_progress.ppt

14:15 - 14:45 – Investigation, Study, Assay (ISA) and how it is used to record and link experiments, Data and SOPs in SysMO-DB Katy Wolstencroft sysmo-isa.ppt

14:45 - 15:30 - ISA and how it could be applied to models Stuart Owen modelsandisa.ppt

16:00 - 17:00 - Talk by Edda Klipp “Computational Systems Biology - Different modelling strategies for different purposes”

9:00-10:00 Models and linking to data summary

10:30-11:00 Talk by Jacky Snoep “JWS Online's face-lift: incorporation of SBGN and linking to the outside world” jwsupdate.pdf

11:00-11:30 Talk by Falko Krause “MIRIAM annotations and how semantic SBML can help” semanticsbml_annotation.pdf

11:30-12:30 Interactive sessions: a) Miriam annotation and tooling– Falko Krause b) Model building and testing with SBML and JWS online – Jacky Snoep and individual participants

A report summarising the meeting can be found here: linkingdatatomodels2.doc

1. The SysMO-DB team will provide and maintain a recommended list of vocabularies and database resources for annotation within SysMO.
2. The SysMO SEEK will be extended to allow models to be described as part of the ISA infrastructure. The workshop participants concluded that the models should be linked at the Assay level.
3. The mechanism for linking models and data should contain information about which data was used for model construction and which data was used for model validation.
4. Workshop participants will send Falko Krause examples of model files so he can further develop his ideas surrounding annotation of non-SBML models

SysMO Consortium Members: Carolyn Lam, Peter Goetz, Sebastian Henkel, Maksim Zakhartsev, Falko Krause, Jay Moore, Sylvia Haus, Simon Borger, Maria Nikolakakou, Tobias Fürch, Gong Zhang, Susanne Gerber, Mark Musters

SysMO-DB: Stuart Owen, Katy Wolstencroft and Jacky Snoep

MCISB: Daniel Jameson and Neil Swainston