How Neurocytes, Stereocytes, Senseocytes, Stemocytes work

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How Neurocytes, Stereocytes, Senseocytes, Stemocytes work

Post by bwisialo » Wed Aug 17, 2016 8:07 pm

Nuerocytes and Balloons

Neurocytes produce the signal substances that you select. S1, S2, S3, and S4 are signal substances. In the Oscillator preset, they correspond to the channel selection: channel 1 is S1.

The signal substances go from the Neurocyte into connected cells. If signal substances are going into a Buoyocyte, you can make the Buoyocyte's Density be based on the amount or "concentration" of signal substance in the Buouyocyte.

When you tap the "..." button next to the Buouyocyte's Density setting, you can choose values to determine how the signal substance will affect the Density. You see the default formula: "a x concentration + b." You select values for "a" and "b" and the signal substance The app keeps a running calculation of the "concentration" of signal substance in the Buouyocyte: "concentration" is a number that changes as the signal substance goes into the Buoyocyte and increases, and then diffuses and decreases.

"b" is the Density that the Buoyocyte will have when there is no signal substance in it (a x 0 + b = b). If you leave "b" at 0, the Buoyocyte's Density will simply be: the "concentration" of signal substance in the Buoyocyte multiplied by a factor of "a" (a x concentration + 0). The app multiplies the "concentration" at any given moment by the value you select for "a", and the resulting number will be the Buouyocyte's Density value at that moment.

When you use the "Oscillator preset" to make the Neurocyte oscillate between, for example, S1 and S2, the amount of S1 that the Neurocyte produces goes up and down -- like a sine wave -- from a large positive number to a large negative number, and back to a large positive number, etc.. To see how the value of S1 (and S2) changes, you can use the Neurocyte simulator and the Oscilation visualizer.

If Buoyocyte's Density is based on S1 and "a" = 8.00, the Buoyocyte's Density will go from a large positive number (when concentration is positive) to a large negative number (when concentration is negative), then back to a large positive number, etc.. As a result, the Buouyocyte will sink and rise, sink and rise. Compared to "a" = 4.00, for example, when "a" = 8.00 the shift between maximum and minimum Density will happen more abruptly.

In the "Oscillator preset," you also get to select the "Period" of time the oscillation takes. If you select a low number, S1 will be positive for a short period and then negative for a short period: the Buoyocyte will sink for a short time then rise for a short time. If you select a high number, the Buoyocyte will sink for a long time then rise for a long time.
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Re: Explaining Neurocytes, Stereocytess, Senseocytes, Stemoc

Post by bwisialo » Wed Aug 17, 2016 8:09 pm

Neurocyte-Myocyte-Phagocyte Crawlers (Friction)

See Neuorcytes and Balloons (above) for basics on how Neurocytes, signal substances, and programmable values work.

Myocytes have three values that you can program to be based on the amount of signal substances in the Myocyte: Contraction, Bending, and Lift. In Balloons you only use one of the two substances produced by the Neurocyte's oscillation -- to program Density. For Friction you use both substances: one to program Contraction and the other to program Lift.

If you select S1 and S2 in the "Oscillator preset," S1 and S2 will go up and gown like sine and cosine waves. Imagine that S1 is the green wave, S2 is the red wave, and that this represents one oscillation cycle.
Image
It begins with S1 at its max and S2 is 0. Then S2 hits its max and S1 is 0. Then S1 hits its minimum (a large negative value), followed by S2 at its minimum. You can program Contraction with S1 to make the Myocyte contract and extend, and program Lift with S2 to make it lift up and plant down the cells in front and behind it. The two maximums and two minimums allow the Myocyte to go through a four step cycle. The Myocyte will contract, and at its maximum contraction, it will lift the cell in back, pulling it forward; then it will extend, and at its maximum extension, it will lift the front cell, pushing it forward. This cycle will repeat in sync with Neurocyte oscillation, allowing the organism to move across the substrate.

To see how the values of S1 and S2 change, you can use the Neurocyte simulator and the Oscilation visualizer.

To program Contraction and Lift, use the default formula: a x concentration + b. "b" is the value that Contraction and Lift will have if there is no signal substance in the Myocyte. Suppose you make Contraction based on S1, leave "b" at 0, and set "a" to 4.00; and you make Lift based on S2; leave "b" at 0, and set "a" to 8.00. To get your organism moving at a quick pace, you want the oscillation cycle to be quick: setting the oscillation Period to 1h in the Oscillator preset gives the fastest oscillation.

If your organism moves in the opposite direction than what you want, go to the cell that produces the Myocyte and change corresponding the child angle 180 degrees: rotating the Myocyte 180 reverses the front and back of the Myocyte and makes the organism crawl in the opposite direction.
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Re: Explaining Neurocytes, Stereocytess, Senseocytes, Stemoc

Post by bwisialo » Wed Aug 17, 2016 8:12 pm

Stereocytes and Smart Swimmers

See Neuorcytes and Balloons (above) for basics on how signal substances and programmable values work.

Stereocytes detect stimuli: either Food or Cells, based on the cell color you specify at the bottom of the Stereocyte settings.

A Stereocyte produces signal substance in response to the presence of stimuli, and it detects and produces different output for stimuli on the right and the left. E.g., if you use S1, it will produce +S1 for stimuli on the right and -S1 for stimuli on the left (or vice versa depending on whether you set Output to + or -). The orientation of the Stereocyte matters: the antennae must be on the left and right.

Flagellocyte-Myocyte-Stereocyte-Phagocyte Swimmer

You can program Myocyte Bending to make your swimmer turn left and right, using the default formula: a x concentration + b. "b" is the value that Bending will have when there is no signal substance in the Myocyte: with "b" = 0, your swimmer will swimmer straight when the Stereocyte isn't detecting food.

Two values determine how strongly the Myocyte will bend: the Output value of the Stereocyte and the value for "a" in Myocyte bending. Many combinations for these two values will work. One way to start is to pick a medium values for Output and "a," then watch how your organism behaves. If it turns too much, decrease one (or both) of the values. If it turns too little, increase the value(s). Adjust until you get a combination of values that works well.

If your swimmer is turning away rather than toward food, change the Stereocyte Output value from positive to negative (or vice versa).

Two-Flagellocyte Swimmer (left and right Flaggelocyte)

You can program Flagellocyte Swim force to make your swimmer turn left and right, using the default formula: a x concentration + b.

"b" is the constant speed of Flagellocyte when the Stereocyte is not releasing signal substance. For you organism to swim straight when there's no stimulus, "b" needs to be the same value for both Flagellocytes. "b" cannot be 0: your swimmer will not move forward.

"a" determines how strongly the signal substance will speed up or slow down the Flagellocytes. To get symmetrical left / right turning behavior, "a" needs to be the same value in both Flagellocytes but it needs to be positive in one Flagellocyte and negative in the other.

For example, suppose that the Stereocyte produces +S1 for stimuli on the right, and that the left Flagellocyte has +a and the right Flagellocyte has –a. Here is the behavior that results: when the Stereocyte produces +S1, the swim force of the left Flagellocyte will increase (+a times +concentration + b) and the swim force of the right Flagellocyte will go to the minimum of 0 (-a times +concentration + b). This behavior makes the organism turn / rotate to the right.

Similarly, when the Stereocyte respond to stimuli on the left and produces –S1, the right Flagellocyte speeds up ("-a times -concentration" is positive), the left one stops ("+a times -concentration" is negative), and the organism turns to the left.

You don't have to worry about figuring out the positives and negatives for left and right. Set one Flagellocyte to +a and the other to -a. Then, if your organism turns away from food rather than toward food, change the Stereocyte Output value from positive to negative (or vice versa).

How much your organism turns is determined by Stereocyte output as well as "a." If your organism doesn't turn enough, increase Output. If it turns too much, decrease Output. Or, you can change "a" in both Flagellocytes.
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Re: Explaining Neurocytes, Stereocytess, Senseocytes, Stemoc

Post by bwisialo » Wed Aug 17, 2016 8:14 pm

Senseocytes and Stemocytes

See Neurocytes and Balloons (above) for basics on signal substances and programmable cells.

Senseocytes detect stimuli: either Food or Cells, based on the cell color you specify at the bottom of the Senseocyte settings. Unlike a Stereocyte, a Senseocyte produces the same output regardless of the direction of the stimuli. For example, a Stereocyte with Output set to 5.0 will produce output like this:

5.0 when stimulus is directly to the right
-5.0 when stimulus is directly left
0 when stimulus is directly ahead or directly behind

An equivalent Senseocyte will have an output of 5.0 whether the stimulus is right, left, ahead or behind. You can use a Senseocyte when you want signal substance of a particular value to be produced regardless of the direction of the stimulus. See example below.

A Stemocyte will remain a Stemocyte until it is triggered by a signal substance to "differentiate" or change into another cell in the genome.

For example, suppose you want an M6 Stemocyte to change into your M7 cell whenever the Stemocyte is near a blue cell. You can do this with a Senseocyte attached to the Stemocyte.

Set the Senseocyte to produce S1 when it detects blue cell. Set the Stemocyte to differentiate into M7 in the path 1 setting: the Stemocyte changes into the M7 cell when the value for path 1 is greater than .5. Program the Value for path 1 and select the inequality formula: value = a if concentration < c; value = b if concentration > or = c. Use a = 0, b = 1, c = .01.

Here is the resulting behavior. When the concentration of S1 in the Stemocyte is below .01, the value for path 1 will be 0; and when the concentration is .01 or higher, the value will be 1 ("b"). Whenever the Senseocyte detects a blue cell and produces S1, the Stemocyte will change into the M7 cell.

You can use a second Senseocyte producing S2 to, for example, make the Stemocyte turn into your M8 cell in path 2 when that Senseocyte detects green. The Stemocyte turns into M7 when near blue and M8 when near green.

You can change the sensitivity of the cell change by changing the Senseocyte Output and or "c."
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Re: Explaining Neurocytes, Stereocytess, Senseocytes, Stemoc

Post by bwisialo » Wed Aug 17, 2016 8:23 pm

A note from Petter :)
Petter wrote:Nice explanations :). A few things worth pointing out, negative concentrations were mentioned which might seem unphysical. The concentrations we talk about are all relative to some "normal" level in the cells. So if the "concentration" of S1 is negative, we mean that it is lower than it's normal value. We could have kept actual concentrations that were always positive in the game but then the settings would have been more complicated since if you want the swimmer to turn towards food insted of away from it you can't just change the sign.

Another thing worth mentioning is that the signal substances diffuse through all cells, except lipocytes. These are supposed to be able to act kind of like glial cells in our bodies. Lipocytes can though have a non-zero concentration from it's parent and it's children can be affected by it. Nothing can though diffuse into or out of them. This means that when you use the oscillator preset and are entering the number of connected cells, you shouldn't count the lipocytes. Enter the number of connected non-lipocyte cells.
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Re: Explaining Neurocytes, Stereocytes, Senseocytes, Stemocy

Post by Reaper Elite » Mon Aug 29, 2016 2:15 am

Yo petter could you make it so we could control the signal substance pathways with a genome diagram so it would send the signal substance where it's needed without wasting it where it's not needed. (Optional neuro/senso/stereo control pathway tab)



Ps. if you don't want/need to that's fine, no prob.
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Re: Explaining Neurocytes, Stereocytes, Senseocytes, Stemocy

Post by Delupara » Thu Sep 22, 2016 12:34 pm

I was testing the stereocytes out on a sandbox substrate, more specifically the cell sensing area. However they don't seem to react to any cell that I placed next to their antennas. Any idea how? I made sure that the output was maxed out and that the colors matched up. What gives?
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Re: Explaining Neurocytes, Stereocytes, Senseocytes, Stemocy

Post by Alast » Thu Sep 22, 2016 12:52 pm

Color Threshold needs to be greater than 0, so it has to be 0.01 at least with the first Snap Value being 0.07
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Re: How Neurocytes, Stereocytes, Senseocytes, Stemocytes wor

Post by GreenTom » Thu Nov 03, 2016 7:02 pm

Is there anything to do to get the neurocyte oscillators to start? I'm seeing a problem where oscillators don't start up--that is, the colored lights don't flash, and they don't trigger actions in nearby cells.

Pretty sure this isn't user error, as the exact same neurocyte does work if I rearrange it a little bit. See the attached picture. The two organisms use the same neurocyte (M2), the only difference is parentage. The left organism was M1 -> M2, the right one was M1-> M15 -> M2. The left one works fine, but if you look, the neurocyte on the right one is not firing. I did try this both without changing M2 and changing M2's oscillator from 2 connections to 3 connections. Same results both ways.

(M15 is just a photocyte put in to delay the neurocyte, as early muscle movement was tearing the half-formed creature apart).
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Re: How Neurocytes, Stereocytes, Senseocytes, Stemocytes wor

Post by bwisialo » Fri Nov 04, 2016 6:46 am

Two options. Make the cell that produces the oscillating Neurocyte be a Neurocyte with all channels at S1 max output. Second option: on the first S1 channel, change "b" from 0 to .82, or whatever the smallest positive value is. Do either of those work for your organism?
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