Workshop: Linking Models and Data in SysMO Katy Wolstencroft, SysMO-DB University of Manchester, UK

Outline The modelling process Relating data and models Where did the data come from for developing the model? Where did the data come from for validating the model? What were the results of model simulations? What you do in your own projects? Storage, sharing How you publish models?

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

SysMO-DB Framework Sharing information between experimentalists and modellers.

Sharing in SysMO-SEEK A Catalogue of SysMO assets SysMO Yellow Pages The people and their expertise The institutions and their facilities Data – experimental data sets Data – analysed results Data – external reference data sets Models Model simulation results Processes – laboratory protocols and bioinformatics analyses The catalogue references assets held elsewhere

Information management and exchange Within project Across SysMO consortium Public Within Group Personal

Experimentalists Data capture from instruments Data generation and storage Primary data analyses Capture and management of derived data from primary analyses Link data to public and pre- existing resources Interpretation Modellers Obtain specific results for model construction and parameterisation Obtain specific results for model validation Creation and validation of models Management of models and their results Link results to public and pre- existing resources

Modellers Exchange Experimentalists Exchange Bioinformaticians

Data in context JERM “Just Enough Results Model” Minimum information to exchange data What type of data is it Microarray, growth curve, enzyme activity… What was measured Gene expression, OD, metabolite concentration…. What do the values in the datasets mean Units, time series, repeats…. Which experiment does it relate to How was the data created SOPs and protocols Harvesting standards, current practice and consortium schemas and spreadsheets ISA-TAB

ISA-TAB Investigation, Study Assay Data in the context of the experiment(s) that produced it Experiments range from one assay to complex multi-assay studies employing one or more technologies in combination

Models Models can be shared in SysMO-SEEK in any format SBML is the recommended format SBML models can be simulated in JWS Online Still to do: Models and data association Models in their experimental context

In the Community Models can be published in public repositories JWS Online, BioModels Models can be annotated SBML, MIRIAM, SBO Currently no public resources for sharing models with associated data

Today Examples of modelling practices Jacky Snoep Neil Swainston and Daniel Jameson (MCISB) Discussion about your modelling practices Looking at data management in SEEK and the ISA framework Could ISA be used for relating models and data?

Acknowledgements SysMO-DB Team SysMO-PALS myGrid, EML and JWS Online teams OMII-UK, Uni Southampton EMBL-EBI, MCISB

Summary

JWS Online Data from SEEK should be made available in JWS online simulator Promotion of SBML and overcoming tooling problems Look into libSBML and SBToolbox for matlab conversion Identify problems for simulating SBML in JWS Online

Annotations Lists of recommended databases and controlled vocabularies should be made available for SysMO Guidelines for specificity MIRIAM.csv file in SEEK

ISA Linking Models and data should be separated at the assay level Models and experimental work can then be part of the same study Assay types need to be extended to include types of models Clear distinctions should be made between construction and validation data

Tools Kinetics wizard JWS Online Key Results Semantic SBML