Team:BCCS-Bristol/Modeling-Hybrid

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Latest revision as of 14:47, 28 October 2008

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Hybrid Model - BSim v2

To get help improve the accuracy of the agent based model and bring together inter and extra cellular activities and processes, the hybrid model model forms the integrating step. Unfortunately, time did not permit completing this part of the modelling during the 2008 entry, so instead this has been considered as the next release of BSim - Version 2. The new version will not only incorporate the GRN and agent based models into a single framework, but also include additions and improvements that have arisen during use of the current system.

Specification

ID	Feature	Description
1	Incorporation of GRN in agent based model	Each of the modelling approaches have been considered in separate contexts, mainly due to the differing aspects of the system they are concerned with. Now, having working models for each, it would be possible to bring these together with the aim of improving simulation accuracy and allowing for the internal cellular dynamics to be studied in an ever changing physical environment. Such a hybrid model may also help shed light on the critical aspects of project as a whole.
2	Large Scale Simulations	We have been able to run simulations with several thousand bacteria, however, these generally took several days to complete. When compared with standard wet lab assays, to get a similar simulated bacteria density only a small area could be considered. It would be interesting to run simulations of a significant size and bacteria density to see how well the simulations match realworld behaviours. Obviously this could be achieved by running simulations for longer periods, however, it may be beneficial to update the BSim framework to make use of fully distributed computing architectures, via toolkits such as MPI.
3	Advanced Adhesion Models	Although the basic method of adhesion showed bacteria chemotaxis was not impacted, it would be useful to incorporate more advanced models to confirm that these also do not affect overall particle movement. These could include fixed adhesion, where bacteria are stuck to points on a particle and can impart rotational forces, or the restriction of adhered bacteria tumbling angles to limit the direction of movement. Additionally, simulations could include free swimming bacteria to verify that adhered bacteria impart the majority of force on the particles.
4	Population Dynamics	It has been assumed that bacteria do not replicate or die in our system. Although valid for short time periods, in simulations of a longer duration population dynamics may become an important factor. Incorporating this behaviour would also make the simulation framework suitable for wider areas of bacteria study, specifically in understanding colony dynamics related to growth and movement.
5	Complex Adaptive Structures	One of the initial future aims of the project was to incorporate the idea of complex adaptive behaviour, allowing structures to autonomously alter their shape based on environmental cues. Directing particle movement was a first step towards this aim. Another could be to include the idea of a division of labour. Using simple rules to define the behaviour of specific problem elements, for example particle movement, structure design and team management, our framework could help evaluate the emergence of additional behaviours from the interactions between differing bacteria types.

@@ Line 21: / Line 21: @@
 ===Specification===
+{| class="bccstable" align="center"  margin-left="40px"
+| align="center" width="3%" style="background:#f0f0f0;"|'''ID'''
+| align="center" width="27%" style="background:#f0f0f0;"|'''Feature'''
+| align="center" width="70%" style="background:#f0f0f0;"|'''Description'''
+|-
+| 1
+|| Incorporation of GRN in agent based model
+|| Each of the modelling approaches have been considered in separate contexts, mainly due to the differing aspects of the system they are concerned with. Now, having working models for each, it would be possible to bring these together with the aim of improving simulation accuracy and allowing for the internal cellular dynamics to be studied in an ever changing physical environment. Such a hybrid model may also help shed light on the critical aspects of project as a whole.
+|-
+| 2
+|| Large Scale Simulations
+|| We have been able to run simulations with several thousand bacteria, however, these generally took several days to complete. When compared with standard wet lab assays, to get a similar simulated bacteria density only a small area could be considered. It would be interesting to run simulations of a significant size and bacteria density to see how well the simulations match realworld behaviours. Obviously this could be achieved by running simulations for longer periods, however, it may be beneficial to update the BSim framework to make use of fully distributed computing architectures, via toolkits such as MPI.
+|-
+| 3
+|| Advanced Adhesion Models
+|| Although the basic method of adhesion showed bacteria chemotaxis was not impacted, it would be useful to incorporate more advanced models to confirm that these also do not affect overall particle movement. These could include fixed adhesion, where bacteria are stuck to points on a particle and can impart rotational forces, or the restriction of adhered bacteria tumbling angles to limit the direction of movement. Additionally, simulations could include free swimming bacteria to verify that adhered bacteria impart the majority of force on the particles.
+|-
+| 4 || Population Dynamics
+|| It has been assumed that bacteria do not replicate or die in our system. Although valid for short time periods, in simulations of a longer duration population dynamics may become an important factor. Incorporating this behaviour would also make the simulation framework suitable for wider areas of bacteria study, specifically in understanding colony dynamics related to growth and movement.
+|-
+| 5 || Complex Adaptive Structures
+|| One of the initial future aims of the project was to incorporate the idea of complex adaptive behaviour, allowing structures to autonomously alter their shape based on environmental cues. Directing particle movement was a first step towards this aim. Another could be to include the idea of a division of labour. Using simple rules to define the behaviour of specific problem elements, for example particle movement, structure design and team management, our framework could help evaluate the emergence of additional behaviours from the interactions between differing bacteria types.
+|}