1. RoSBM Registry of Standard Biological Models Barry Canton (MIT) Vincent Rouilly (Imperial College) Registry Workshop November 2007,Boston

2. RoSBM Biological Systems Need Models! Michigan iGEM Team ‘07

3. RoSBM Challenges Modeling takes time, expertize Weak adoption of standards for model construction Models hard to share, reuse (Sound familiar?)

4. RoSBM Challenges Building takes time, expertize Weak adoption of standards for system construction Parts hard to share, reuse

5. RoSBM Registry of Standard Biological Parts http://parts.mit.edu

6. RoSBM Registry of Standard Biological Models http://openwetare.org/wiki/RoSBM

7. RoSBM Wiki Modeling & the Parts Registry Project 1 -models- Project 2 -models- Project 3 -models- Project 4 -models- Project 5 -models- Parts

8. RoSBM Wiki Modeling with Parts & Models Registries Project 1 -models- Project 2 -models- Project 3 -models- Project 4 -models- Project 5 -models- Parts Models

9. RoSBM Wiki Open data sharing Project 1 -models- Project 2 -models- Project 3 -models- Project 4 -models- Project 5 -models- Model Predictions Experimental Data Parts Models

10. RoSBM CellML Database http://www.cellml.org/models

11. RoSBM Biomodels Database http://www.ebi.ac.uk/biomodels/

12. RoSBM Asmparts software http://soft.synth-bio.org/asmparts.html

13. RoSBM MIRIAM initiative

14. RoSBM RoSBM Motivations / Mission to gain a deeper understanding of the function of BioBricks. to promote the re-usability of BioBrick models. to explore through simulations the properties of de-novo assemblies of parts. to progress towards a faster/cheaper development process. to complement the open-source spirit of Synthetic Biology and open-up a new form of in Silico contributions.

15. RoSBM What Do We Want the RoSBM to Do? Store, Search, Annotate, and Curate models of standardized biological parts. Provide a one-to-many match between DNA biological parts and models. Interface with CAD tools.

16. RoSBM BioBrick Characterization

17. RoSBM BioBrick Characterization Smax=XXX N=1.2 ExperimentsModeling Early experiments to estimate dynamic range of AHL and general response More experiments to improve estimation Of parameters Define Model Fit Model on Data Predict next best experimental points Fit model on new data

18. RoSBM GFP(t) = f(AHL,LuxR,t) One part, many models? BBa_T9002 GFP = f(AHL) GFP(t) = f(AHL,mRNA LuxR, P LuxR, mRNA GFP, P LuxR, RNAp, Ribosomes, t) Parts Models

19. RoSBM

20. Proof of Concept

21. RoSBM desired relationships Model Part Similar Models Including This one Models Included in this one Bio DB Part category Model category

22. RoSBM Data Connectivity Parts Models Exp.DataSim.Data

23. RoSBM Data Connectivity Parts Models Exp.DataSim.Data

24. RoSBM Data Connectivity Parts Models Exp.DataSim.Data

25. RoSBM Data Connectivity Parts Models Exp.DataSim.Data Parts Exp.Data Models Sim.Data

26. RoSBM Thank you! bcanton@mit.edu vincent.rouilly@gmail.com http://openwetware.org/wiki/RoSBM

27. RoSBM ideas Level of abstraction controlled vocabularies Description language MIAGE standard

28. RoSBM Model Curation Machine readable Conform to a description standard Make sure the model works Referencing author, publications, contact Pointing to biological databases MIRIAM standard

29. RoSBM SBML / CellML Overview SBML model = CellML model = Compartments Species Rules Reactions Events Components Variables: name, init_value, interface, units Math Units Imports

30. RoSBM What is a Biological Part Model? What we mean by Biological Model: –Abstraction of a biological process using a formal mathematical description –Focus on kinetic models –Focus on Ordinary Differential Equations System

31. RoSBM Content Advantages offered by modelling Problems to be addressed A solution to some of the above (Motivations) An example of a model entry in the RoSBM (Scenarii of use) What is a ‘Standard Biological Model’ ? Simple Model repository or reusable modeling component. Open issues (level of abstraction, description language, …)

32. RoSBM Current Practices More and more projects explore their project with modelling Matlab, C/C++, Proprietary platform, SBML

33. RoSBM Unused Images