20090219 The case for another systems biology modelling environment

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Jonathan Blakes

2009 ASAP seminar

Technologie

Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Systems Biology ,[object Object],[object Object],[object Object],[object Object],[object Object]

Systems Biology ,[object Object],[object Object],[object Object],[object Object]

Synthetic Biology ,[object Object],[object Object],[object Object],[object Object]

BioBricks ,[object Object],[object Object],[object Object],[object Object],Canton B, Labno A, Endy D. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology (2008) 26: 787-793

Modelling formalisms ,[object Object],[object Object],[object Object]

Aguda B, Goryachev A. From Pathways Databases to Network Models. ISMB 2006 Formalism-space qualitative ↔ quantitative continuous ↔ discrete mechanistic ↔ symbolic ODE stochsim Petri Nets Boolean networks Process calculi BaN

Established approaches ,[object Object],[object Object],[object Object],[object Object]

Recent developments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Computational Modelling Formalisms ,[object Object],[object Object],[object Object],[object Object],[object Object]

Petri nets ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Process calculi ,[object Object],[object Object],[object Object],[object Object]

Graphical S π ,[object Object],[object Object],[object Object]

Kappa ,[object Object],[object Object],[object Object],[object Object],[object Object]

P systems ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Cellular automata ,[object Object],[object Object],[object Object],[object Object]

Support Tools ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Systems Biology Graphical Notation ,[object Object],[object Object],[object Object],[object Object],[object Object]

Goals for a new tool ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Implementation ,[object Object],[object Object],[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Acknowledgements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Macrophage and Bacterium 2,000,000X 2002 Watercolor by David S. Goodsell

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