Slides for the talk given at Plone Conference 2012.

1. Plone 2012
M.A. Guravage — CWI
RepoSE
An On-Line Repository for
Simulation Experiment Descriptions
Arnhem — 10 October 2012

2. systems biology
thesis
h ypo
t i
en
n
si
im
gh
er
t
exp
is
ys
da
al
ta
n
a
modeling

3. turing patterns
Reaction - Diffusion Leaf Venation

4. angiogenesis
Chemotaxis

5. circadian rhythm
PER mRNA TIM mRNA
Normal Limit Cycle Chaotic Limit Cycle

6. obstacles to reproducibility
Growing number of experiments
Increasing complexity of models
Incomplete descriptions
Erroneous descriptions

7. reproducibility initiatives

8. encouraging reproducibility
Specify Minimum Requirements
Minimum Information Requested In the Annota-
tion of Biochemical Models (MIRIAM)
Minimum Information About a Simulation Exper-
iment (MIASE)
Simulation Experiment Description Markup Lan-
guage (SED-ML)

9. what is sed-ml
An XML schema
30+ UML classes
A recipe
An exchange format
Executable

10. a simple sed

11. what is repose
Content types that represent the SED-ML schema
Workflows tailored to an academic audience
Domain-specific meta-data, e.g., KiSAO
SED-ML compliant XML

12. friendlier user interface
<?xml version="1.0" encoding="UTF-8"?>
<sedML version="1.0",
xmlns="http://www.miase.org">
<listOfModels>
<model
id="virtual-leaf-framework"
language="source-code"
name="Virtual Leaf Framework"
source="code.google.com/p/virtualleaf"/>
<model
id="ck-plugin" language="source-code"
name="CK Plugin"
source="code.google.com/p/virtualleaf"/>
</listOfModels>
<listOfTasks>
<task
id="task-d0-1e-8"
modelReference="virtual-leaf-framework,
ck-plugin"
name="Task - D0 is 1e-8"
simulationReference="simulation-d0-1e-8"/>
<task
id="task-d0-1e-6"
modelReference="virtual-leaf-framework,
ck-plugin"
name="Task - D0 is 1e-6"
simulationReference="simulation-d0-1e-6"/>
</listOfTasks>
...
</sedML>

13. what are reopse's goals
Improve the long-term reproducibility of
simulation experiment descriptions
Make SEDs more readable
Make SEDs more accessible
Make SEDs more reliable

14. the whole schema

15. archgenxml
Model directly from the SED-ML standard
Many different content types
The schema makes heavy use of references
The quickest route from concepts to code

16. control access - guide curation
show
private start hidden
conceal
publish-internally
submit retract/reject
retract/reject
retract/reject
internal pending
publish-internally
publish-externally
publish-externally external

17. zope component architecture
Instrumental in adding RepoSE functionality
SED-ML import - z3c.form
SED-ML parser
Model parsers, e.g., SBML
Simulation Web Services

18. addons
ATVocabularyManager
Plone4Artists Subtyper
P4A.fileimagez
P4A.videoembed
POI

19. generic setup
Add custom indicies to the catalog
Install and configure placefull workflows
Creates default roles and permissions
Creates default repository
Add portal tabs

20. deployment – buildout
Varnish caching proxy
5 ZEO Clients
Zeo Storage Server
Log rotation
Supervisor process control

21. the future
Create a ReopSE hierarchy from a SED-ML file
Make Model details available during composition
Execute SEDs without leaving RepoSE
Improve navigation

22. conclusion
Plone was quickest route from concepts to code
Python and Plone provided the right tools
Without Plone, RepoSE would not have been built

23. acknowledgments

24. Thank You

25. Questions?