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

Modellers

Exchange

Experimentalists

Exch

ange

Exchange

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-TABInvestigation, 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