Saturday, August 8, 2009

Modeling (Membrane Computing) Update

Hi Everyone!

This will be our first update on Membrane Computing (MC) and agent-based approach to model our complex biological system.

In regards to modeling of Autoinducer-II Quorum Signaling, we have been able to successfully complete our implementation of this signaling cascade. Monitoring each cell as an agent, we are able to monitor the system at both, cell level and population level.

Currently our simulation uses a well known algorithm called Gillespie's Algorithm. In simple words, the Gillespie algorithm keeps stochasticity (randomness) in our simulation. Why is it important to have this randomness in our model? Because this will push our model one step closer to actual biological system. Because cells don't interact with each other or their environment at discrete steps. As an example consider protein-protein interactions versus cell division. These two interactions have quite different time scales. Our implementation of Gillespie Algorithm takes care of accounting for such cases.

At this stage our model is able to produce concentration graphs and allows user to review how the system behaves at the cell level and also at colony level. We are working on implementing powerful visualizations and a user-friendly interface for our model.

We are also working on addition of new updating scheme for cells during simulation. Currently our algorithm updates state of each cell at single steps. It is worth mentioning that because of the way our Gillespie Algorithm is setup, time delays between each step can be as short as 0.0001 second (considered instantaneous) or a given step could take as long as one minute. This will compensate for different interactions and the time it takes for each interaction to complete. The second scheme which we are working now to complete hopefully before aGEM is where all cells in the system are updated at the same time. This allows cells to be in sync when applying interactions. With single-step updating scheme, as the number of cells increase over time, it takes longer and longer for cells to update their state based on changes in their environment. This side effect of non-synchronous updating scheme only kicks in when we have high population of cells. Since we have introduced cell division to our simulation where our system could start with one cell and end up with 300, a synchronous updating system could take us one step closer to how the actual biological system works.

We will post updates at least once a week on our current progress; We also hope to have some screen shots on our visualizations and interface in near future.

Thanks for following our progress :)

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