Intro

Here are a list of resources for large scale neural simulations. I am particularly interested in knowing if there is any value in trying to get the NEURON platform to run as a massively parallel job on an FPGA or even a family of interconnected FPGAs. It would seem like simulating large populations of neurons is an ideal project for parallelization. Feel free to add your thoughts. In addition to adding links, it would be helpful to add a few brief sentences under each tab giving your thoughts or a brief summary.

Primary Resources

• A book on parallel simulation of large scale neuronal clusters.
• Research paper (2006): A Component-Based FPGA Design Framework for Neuronal Ion Channel Dynamics Simulations
• Research paper (2007): Methodology and Design Flow for Assisted Neural-Model Implementations in FPGAs

[From the Neurodudes link below] After 2007 paper [above], the first author, Randall K. Weinstein, became the co-founder and Chief Systems Architect of http://www.simatratechnologies.com/. A search over NIH awarded grants reveals grant 1R43NS057859-01 for “A low-cost, high-speed platform for neural modeling”, which this page suggests may be worth on the order of $183,163 for 2007 (or maybe that’s the amount that has already been dispensed? or the amount left?). Description of the grant:

Neural models, mathematical descriptions of neural behavior, are an invaluable tool for developing new medical treatments and understanding how the nervous system works. But as researchers discover more information about the nervous system, these models become more complicated. As a result, many modern neural models require powerful computer hardware, such as supercomputers, in order to be simulated and studied. Unfortunately, these systems are expensive and difficult to use. This project will create a low-cost, user-friendly, and computationally powerful system for neural modeling based on a technology called field-programmable gate arrays (FPGAs). This project will develop the user-friendly tools for creating neuron models on FPGAs, and the high-speed interface that will maximize the computational power of FPGAs.

• Faster neural simulations with FPGAs: Post on Neurodudes Blog
• Current performance measurements for NEURON: Migliore, M., Cannia, C., Lytton, W. W., Markram, H. & Hines, M.L. (2006). Parallel network simulations with NEURON.. J Comput Neurosci, 21, 119-29.
• Simulation of networks of spiking neurons:review of tools and strategies (Brette 2007)
• Programmable Logic Construction Kits for Hyper-Real-Time Neuronal Modeling (Guerrer 2006)
• Advancing the Boundaries of High-Connectivity Network Simulation with Distributed Computing – (Morrison 2005)

Other Relevant Resources

• Rich’s post summarizing Neural Simulators
• NIH Program Announcement for Exploratory Innovations in Biomedical Computational Science and Technology