Our foray into Julia was mostly motivated by a desire to have a programming language as fast as C but as easy to program as Matlab. In particular, we need really fast looping speed, which is necessary to simulate dynamical systems. Our particular project involves fitting a conductance-based model (i.e. Hodgkin-Huxley-like equations) to some data using MCMC. We’re not trying to fit the precise spike shapes per se but the firing rates of synaptically coupled pools of neurons in response to various inputs. We thus need to run simulations for some time, compare the averaged rates to previous runs, and iterate. For good fits, we may need to do this a million times. Hence, we need speed and we can’t really parallelize because we need information from one iteration before going to the next.
Now, one would think that simulating neural networks is a long solved problem and I thought that too. Hence, I instructed my fellow Wally Xie to look into all the available neural simulators and see what fits the bill. We first tried Neuron but couldn’t get all of it to work on our Linux machine running CentOS (which is what NIH forces us to use). We were met with incredulity and dare I say hostility when we suggested such to the Neuron authors. That was the end of Neuron for us. We next tried Nest but found it difficult to specify the neuron model. We finally settled on Brian, which is adaptable, written in Python, and supported by very nice people, but is turning out to be too slow. Native Python is also too slow. Stan would be great but it does not yet support differential equations. Wally is now implementing the code in Julia, which is turning out to be very fast but has a possible bug that is preventing long runs. The developers are extremely helpful though so we believe this will be worked out soon. However, it is hard to get plotting to work on Julia and as pointed out by many, Julia is not nearly as complete as Python or Matlab. (Yes, Matlab is too slow). We could use C and will go to it next if Julia does not work out. Thus, even though people have been developing neural simulators for decades, there is still an unmet need for something adaptable, fast, easy to use, and runs out of the box. A neuro-Stan would be great.
