David Lung

People also want to have access to raw data files (connection_buffer.txt, muscles_activity_buffer.txt, position_buffer.txt, worm_motion_log.txt, *.dat). Copy files based on a list of filenames. Define some keywords like SIBERNETIC_RAW or ALL

The function to plot the connection matrix already exists. We just need to call it.

Replace xvfb

1

Xvfb cannot be accelerated by a GPU. I think that's the reason why the rerun and recording of a prev simulation is so slow (1-2 FPS) Maybe we should switch...

Optimize for N epochs. Invoke custom callback at the end of an epoch.

4

I want to propose some changes but I am not entirely sure where they would fit best. Let's assume there is an iterator for a training set. Often, the suggested...

Sometimes nrniv tasks don't get terminated after CTRL+C

2

If I interrupt the optimizer at a certain point, multiple nrniv tasks remain running. A sigint handler at the right place should do the trick.

Add param so we can run a prev simulation starting from a specific ti…

3

…mestep.

Do not merge! Just for testing purposes and discussions.

Pressure buffer file issue

6

What particles are supposed to be written to the pressure file? The file should only contain particles belonging to the body of the worm, right? If that is the case,...

With that [PR](https://github.com/SciML/SciMLBase.jl/pull/85) I can index into an `ODESolution` using a `Num` The following code raises an `BoundsError: attempt to access Tuple{Int64} at index [0]` ``` using ModelingToolkit using ModelingToolkit:...