workshop: linking models and data in sysmo
DESCRIPTION
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? - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/1.jpg)
Workshop: Linking Models and Data in SysMO
Katy Wolstencroft,SysMO-DB
University of Manchester, UK
![Page 2: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/2.jpg)
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?
![Page 3: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/3.jpg)
Aims
Gather requirements for model management in SysMO-SEEK
Work out common practices and determine “Just enough” for publishing and sharing in SysMO-SEEK
![Page 4: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/4.jpg)
SysMO-DB Framework
Sharing information between experimentalists and modellers.
![Page 5: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/5.jpg)
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
![Page 6: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/6.jpg)
![Page 7: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/7.jpg)
Modellers
Exchange
Experimentalists
Exch
ange
Exchange
Exchange
Bioinformaticians
![Page 8: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/8.jpg)
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
![Page 9: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/9.jpg)
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
![Page 10: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/10.jpg)
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
![Page 11: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/11.jpg)
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
![Page 12: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/12.jpg)
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?
![Page 13: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/13.jpg)
Acknowledgements SysMO-DB Team SysMO-PALS
myGrid, EML and JWS Online teams OMII-UK, Uni Southampton EMBL-EBI, MCISB
![Page 14: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/14.jpg)
Summary
![Page 15: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/15.jpg)
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
![Page 16: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/16.jpg)
Annotations
Lists of recommended databases and controlled vocabularies should be made available for SysMO
Guidelines for specificity
MIRIAM.csv file in SEEK
![Page 17: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/17.jpg)
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
![Page 18: Workshop: Linking Models and Data in SysMO](https://reader035.vdocuments.site/reader035/viewer/2022062518/568145b8550346895db2c11c/html5/thumbnails/18.jpg)
Tools
Kinetics wizard JWS Online Key Results Semantic SBML