plasticity: plasticity pre-beta

This is the pre-beta release of 'plasticity'. All phase-1 milestones have been achieved. In general terms, these were to develop a neuron modeling-framework with the following components/functionality specs...

• create 3D surface meshes representing dendritic segments
• simulate stochastic diffusion of receptor-particles along the mesh surface
• simulate actin filament dynamics inside the spine regions of the dendritic mesh
• simulate scaffold-associated protein (sap) clustering at sub-synaptic spine regions
• simulate the multivalent interactions of sap
  • sap-sap
  • sap-actin
  • sap-glur
• specify rate, affinity, concentration, and other parameters affecting biodynamics
  • parameters have downstream effects on clustering, polymerization, diffusion etc.
• optimize graphics to handle real-time simulations
• simultaneous rendering of all model components in 3D space
  • spatial relationships between components are meaningful
• parameters can be set via graphical interface or edited directly within the source code
• fully open source code

Overall, the idea was to create a modeling framework that allows neuroscientists, whether novice or expert programmers, to simulate molecular-level neural dynamics. Simulations can be run via a graphical interface that hosts a myriad of adjustable parameters; naturally, directly modifying the source code is also an encouraged option.

The next phase of development is the synthesis an advanced 'multiplex module schema'. In plain terms, we want an actin module for actin experts, a particle diffusion module for diffusion experts, a meshing module for morphology experts, a receptor/sap dynamics module for scientists with expertise molecular-level synaptic plasticity, and so forth. In a sense, the individual modules are intended to be a playground for the possible, with the only restriction being the format of their function inputs/outputs. This will allow a scientist with expertise in, say, AMPA-type receptor diffusion to tinker within the receptor/sap dynamics module and trust that parameters returned from calls to the actin module are accurate, because they have been developed by actin experts. First-things-first, of course, there is still an ample amount of work to be done on the pre-beta release, but this is the direction things are headed with 'plasticity'. For more notes, check out: http://bradleymonk.com/plasticity