Workshop linking models and data in sysmo
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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?

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Workshop: Linking Models and Data in SysMO

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Workshop linking models and data in sysmo

Workshop: Linking Models and Data in SysMO

Katy Wolstencroft,

SysMO-DB

University of Manchester, UK


Outline

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?


Workshop linking models and data in sysmo

Aims

  • Gather requirements for model management in SysMO-SEEK

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


Sharing information between experimentalists and modellers

Sharing information between experimentalists and modellers.

SysMO-DB Framework


Sharing in sysmo seek

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


Workshop linking models and data in sysmo

Experimentalists

Modellers

Exchange

Bioinformaticians

Exchange

Exchange

Exchange


Data in context

Data in context

JERM

  • 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

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

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

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

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

Acknowledgements

  • SysMO-DB Team

  • SysMO-PALS

  • myGrid, EML and JWS Online teams

  • OMII-UK, Uni Southampton

  • EMBL-EBI, MCISB


Summary

Summary


Jws online

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

Annotations

  • Lists of recommended databases and controlled vocabularies should be made available for SysMO

  • Guidelines for specificity

  • MIRIAM.csv file in SEEK


Isa linking

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

Tools

  • Kinetics wizard

  • JWS Online

  • Key Results

  • Semantic SBML


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