THEORETICAL SYSTEMS IN BIOLOGY: TISSUES & ORGANS
CONTENTS INTRODUCTION COMPLEX BIOLOGICAL SYSTEMS, MODELLING AND MODEL INTEGRATION NATURE TO NUMBERS: COMPLEX SYSTEMS MODELLING OF CANCER MATHEMATICAL MODELLING IN TUMOUR SYSTEMS BIOLOGY GROWTH MODELS ANGIOGENESIS MODELS TREATMENT RESPONSE MODELS MODELLING METHODOLOGIES DYNAMIC PATHWAY MODELS OTHER MODELS SUMMARY CONCLUSION COPING WITH COMPLEXITY: MODELLING OF COMPLEX SYSTEMS PREAMBLE DYNAMIC COMPLEX SYSTEMS PROPERTIES OF COMPLEX SYSTEMS A SYSTEMS-THEORETIC APPROACH IN BIOLOGY: SYSTEM BIOLOGY INDIVIDUAL-BASED MODELLING METHODS SIMULATION SOFTWARE COMPLEXITY AND MODEL INTEGRATION: FORMALISATIONS THE NATURE OF MODELS ABSTRACT VIEWS OF MODELS MODEL INTEGRATION: PREVIOUS WORK MODEL INTEGRATION IN MANAGEMENT AND ENVIRONMENTAL SCIENCES MODEL INTEGRATION IN SYSTEMS BIOLOGY NOVEL STRATEGIES FOR INTEGRATING MODELS INTO SYSTEMS-LEVEL SIMULATIONS MOTIVATION NOVEL MODEL INTEGRATION FORMALISATIONS LINEAR INTEGRATION STRATEGY AGENT-BASED INTEGRATION A KNOWLEDGE-DRIVEN APPROACH (KDA) FOR ADDRESSING MODEL FOCUS AND SCOPE KNOWLEDGE-DRIVEN ABI: A NOVEL FORMAL PROTOCOL FOR MODEL INTEGRATION EXPECTED RESULTS AND VALIDATION EXPERIMENTS IN MODEL INTEGRATION MODEL INTEGRATION EXPERIMENTS KNOWLEDGE DRIVEN APPROACH: BIT-BUILDING CHEN (2004) DE PILLIS (2005) MALLET (2006) MARKUS (1999) ZHANG (2007) ABI: MODEL DECOMPOSITIONS DECOMPOSITION OF THE DI?USION MODEL DECOMPOSITION OF THE GOMPERTZ MODEL KDA+ABI: FORMAL MODEL INTEGRATIONS GOMPERTZ MODEL INTEGRATION WITH ODES AND DISCRETE MODELS DISCUSSION KDA/ABI PERFORMANCE THE KNOWLEDGE-DRIVEN APPROACH REFERENCES