Neurocyte simulator

Here anything Cell Lab related that doesn't fit into the other topics can be discussed.
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wapcaplet
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Re: Neurocyte simulator

Post by wapcaplet » Fri Dec 23, 2016 5:56 pm

I found these visualizations very helpful for understanding what's going on in the neurocyte. Rather than a simple oscillation, it's a kind of feedback loop where the outputs gradually build up based on the four oscillation parameters. The "Oscillator preset" button gives a quick way to initialize settings for the output channels, but if you fiddle with (or even just inspect) any of the four channel settings after using the preset, the preset no longer applies. And if you have customized the output channels, then use "Oscillator preset" again, it will overwrite your customizations when you hit "OK". It took me far too long to realize this. :?

Anyway, I have been playing around with my own in-game visualizations, and found that a myocyte with a non-swimming flagellocyte "pointer" is helping me to see the curves of S1 and S2 with various settings. On this substrate I've set up four different S1/S2 oscillators using Oscillator Preset:

neurocyte-viz-s1-s2.substrate
neurocyte-viz-s1-s2.png
neurocyte-viz-s1-s2.png (7.97 KiB) Viewed 3443 times
Observations:
  • In the first one (top), both myocytes use S1. They move in unison--left goes up and right goes down at the same time.
  • The second one has S1 on the left, S2 on the right. They are slightly out of sync, and follow a "left right (pause) left right (pause)" pattern.
  • The third one has S2 on the left, S1 on the right. As expected, these go more like "left (pause) right left (pause) right" pattern.
  • Fourth (bottom) has both set to S2. Since both use the same channel, they move at the same time, though slightly later than the S1/S1 version.
By playing around with the neurocyte channels, for example using different "a" values for S1 and S2, the "curves" may become steeper. The flagello pointer will stay up or down for a longer period, and transition more quickly or slowly--or not at all, since the feedback loop can lead to either of them getting stuck at maximum or minimum.
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Nayus
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Re: Neurocyte simulator

Post by Nayus » Fri May 05, 2017 6:16 pm

Is it me or none of the links to the simulator work anymore?
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aneson
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Re: Neurocyte simulator

Post by aneson » Fri May 05, 2017 6:34 pm

I've been having the same issue. Does anyone know who to contact for a possible fix?
ruffo
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Re: Neurocyte simulator

Post by ruffo » Fri May 05, 2017 7:10 pm

Nayus wrote:Is it me or none of the links to the simulator work anymore?
They don't :/
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bwisialo
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Re: Neurocyte simulator

Post by bwisialo » Fri May 05, 2017 8:35 pm

That's unfortunate. :( It can't have been all that difficult to set up. Not that I would know how. I would think it was just some graphing software.
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ruffo
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Re: Neurocyte simulator

Post by ruffo » Sat May 06, 2017 12:05 am

I tried to contact Nirahiel... let's see how it goes :)
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wapcaplet
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Re: Neurocyte simulator

Post by wapcaplet » Sun May 07, 2017 2:41 pm

I had saved a modified copy of Nirahiel's HTML neurocyte signal simulator. Was hoping to clean up or enhance it a bit more, but never got around to it. Here it is: https://www.dropbox.com/s/t6fwav87ufur9 ... .html?dl=0
ruffo
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Re: Neurocyte simulator

Post by ruffo » Mon May 08, 2017 2:01 am

wapcaplet wrote:I had saved a modified copy of Nirahiel's HTML neurocyte signal simulator. Was hoping to clean up or enhance it a bit more, but never got around to it. Here it is: https://www.dropbox.com/s/t6fwav87ufur9 ... .html?dl=0
That's awesome!!
Nirahiel said he no longer has a copy, but that he could code it again. It's great that you had a saved copy!
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bwisialo
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Re: Neurocyte simulator

Post by bwisialo » Mon May 08, 2017 6:39 am

Thanks wapcaplet! Good to see you here. :D
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Nirahiel
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Re: Neurocyte simulator

Post by Nirahiel » Mon May 08, 2017 7:26 pm

Hello there everyone !
I thought nobody was using it anymore, that's why I deleted it.

Well, the thing is, after many tries a long time ago, i went to the conclusion that JavaScript doesn't handle float numbers the same way Java does, and certainly not the right way (but these things happens with float numbers anyway).
I could use a JS library to have perfect numbers handling, but I don't know if the results would still be the same as the app's results, as I don't know if Java's number handling is perfect or not.

But I could get back on this project if there's enough interest.

Cheers :)
Nirahiel, code lover since 1995.
Neurocyte simulator
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