Data and Model Management for Systems Biology

Dagmar Waltemathhttp://sems.uni-rostock.de

Slides available from www.slideshare.net/dagwa/

Developing a computational model

… may take a long time

… may involve different research groups

… may involve different tools

… may involve different modeling approaches

… may lead to different versions of a model

… will result in a bunch of files

… will result in a publication

Journals ask for model code

The Physiome Model Repositoryhttps://models.cellml.org/ Yu et al (2011)

BioModelshttp://www.ebi.ac.uk/biomodels-main/ Li et al (2010)

Journals ask for model code

Fig.: Curation and publication processes in BioModels (Figure courtesy Vijayalakshmi Chelliah)

Journals ask for model code

Fig.: Curation and publication processes in BioModels (Figure courtesy Vijayalakshmi Chelliah)

Manage your data throughout(collaborative) projects

Prepare your model-related data for publication

Archive and documentmodel-related data

Get information about a model's evolution

Extract all data related to a modeling result

Find relevant models

Publish Reproduce & Reuse

What data belongs to a model?

Figure courtesy M. Scharm

What data belongs to a model?

Figure adapted from M. Scharm

What data belongs to a model?

● the model(s) themselves● the semantic annotations describing the model and its

components● the simulation setups and model parametrisation● experimental data used to feed the model● result data (tables, figures)● reference publication

+ links between these files

See also: Henkel et al (2015) Combining computational models, … DATABASE

Manage your data

Personal DataLocal Stores

ExternalDatabases

Articles

Standards

SOPs→ Hands on

Slide courtesy Wolgang Müller. See also: Wolstencraft et al (2015) BMC Systems Biology

Prepare for publication

See also: Waltemath et al (2013) Reproducibility of model-based results in systems biology (Springer)

● Export your model in a standard format.

● Annotate model components with links to bio-ontologies.

– Use Gene Ontology, ChEBI etc for entities

– Use SBO for mathematical terms

– Use TEDDY for behavior

– Provide provenance information (model origin, author, creator, modification dates, software)

– Link to original publication

See also: Waltemath et al (2013) Reproducibility of model-based results in systems biology (Springer)

● Provide the simulation recipe for each analysis you describe in the paper.– Simulation setup

– Model parametrisation

– Algorithm used in analysis (Software)

– Output

● Store the simulation setup in standard format.● Try to reproduce the results from the information intended to publish. ● Ask a colleague to try and reproduce the results.

– Every piece of information necessary for that person to reproduce the findings should be included in the supplementary information.

● Pack all necessary data files into an archive format and submit to a public database to receive a URI.

Prepare for publication

Archive your results

See also: Bergmann et al (2014) COMBINE archive and OMEX format. BMC Bioinformatics

● COMBINE Archive

– Zip-like format to bundle all model related files in one place

– Eases the upload of a modeling study to BioModels

– Tells curators what to do with the files (manifest)

– Eases exchange of files with collaborators

→ Hands on

Find models of interest

The safe way The experimental way– Use MaSyMoS to search for

models (through Cypher queries or M2CAT)

– Try ranked retrieval in PMR2

Figure courtesy Vijayalakshmi Chelliah

→ BioModels hands on

Extract reproduciblesimulation experiments

The safe way– Use SEEK for

model management

– Export Research Objects

The experimental way– Create archives with the

COMBINE Archive Toolkit

– Extract archives from MaSyMoS using M2Cat

internet

internet

internet

SEARCHubiquitin

internet

RESULTSEXPORT

EXPORT

EXPORT

EXPORT

Query database for annotations, persons, simulation descriptions

Retrieve information about models, simulations, figures, documentation

Export simulation study as COMBINE archive

Download archive and open the study with your favourite simulation tool

Open archive in CAT to modify its contents and to share it with others

internet

API Commincations enrich your studies with simulation results

Simulate a Study with just a single click

Fig.: Waltemath and Scharm (2015) BTWFigure taken from http://researchobjects.org

Get information about the model's evolution

The safe way– Use SEEK to look at

model versions

– Check releases of BioModels or exposures in PMR2

The experimental way– Compare model versions

using BiVeS

Fig.: Visualising differences between model versions in BiVeS. See also Scharm et al (2015) BIOINFORMATICS.

Fig.: Example of a model's history in PMR2.

SEEK: Data and model management out of the box

● Questions we'll be answering in the afternoon hands on:– What kind of data can SEEK manage?

– How can we manage and simulate models in SEEK?

– What is the ISA-structure?

– How can we share models inside SEEK and how can we export them?

● Please keep the files you generate throughout the SABIO-RK, COPASI, and SYCAMORE tutorials

● Please register at our sandbox version of SEEK: https://denbi-school.fairdomhub.org/projects/3

Thank you for your attention.

● See you later → Please register with SEEK at https://denbi-school.fairdomhub.org/projects/3

● Else → Check out http://sems.uni-rostock.de for further information on how to make your research reproducible.