Introduction to the hands on session on "Standards and tools for model management" at the ICSB 2015. Focus on COMBINE standards, tools for search, version control and archiving. Used management platform is SEEK.

1. Data and Model Management
for Systems Biology
Dagmar Waltemath
http://sems.uni-rostock.de
Slides available from www.slideshare.net/dagwa/

2. 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

3. Journals ask for model code
The Physiome Model Repository
https://models.cellml.org/
Yu et al (2011)
BioModels
http://www.ebi.ac.uk/biomodels-main/
Li et al (2010)

4. Journals ask for model code
Fig.: Curation and publication processes in BioModels
(Figure courtesy Vijayalakshmi Chelliah)

5. 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 document
model-related data
Get information about a
model's evolution
Extract all data related
to a modeling result
Find relevant models
Publish Reproduce & Reuse

6. What data belongs to a model?
Figure courtesy M. Scharm

7. What data belongs to a model?
Figure adapted from M. Scharm

8. 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

9. Manage your data
Personal Data
Local Stores
External
Databases
Articles
Standards
SOPs
→ Hands on
Slide courtesy Wolgang Müller. See also: Wolstencraft et al (2015) BMC Systems Biology

10. 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

11. 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

12. 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

13. 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

14. Extract reproducible
simulation 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
RESULTS
EXPORT
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

15. 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.

16. 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

17. 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.