[crispyambulance]

I don't get it. What do they mean by "3D engine implemented in DNA code"?

> Synthesize the oligonucleotides from the cube3d.dna file.

OK, so you get a long list of oligonucleotides ordered and shipped. Sounds prohibitively expensive, I guess this is a thought experiment or simulation exercise?

> Arrange the test tubes as shown in the diagram below.

OK, Get a microplate with 384 wells (== test tubes).

> Don't forget to provide the initial concentrations according to the table below.

Dump an oligonucleotide solution into each well? According to what table? There is no "table below". Which oligonucleotide in which well?

> Use a pipette to encode the position (row and column) of each tube to start the computation.

A pipette is used to dispense fluid. How does a pipette "encode position"?? Start what computation?

Is this a joke for biology PHD's?

[pallada92]

Yes, this is more like a thought experiment and it will require lots of efforts and money to realize it smoothly in a wet lab.

However, it is far more realizable than some other DNA implementations described in papers.

The idea to publish DNA code on GitHub with CI, tests, linters, badges etc. is obviously a form of joke, but the project itself was done like a serious applied maths research.

[j-pb]

I love that you do actual research in ObservableHQ!

Awesome visualisations and super interesting work! Looking forward to more :D

[lamp987]

>OK, Get a microplate with 384 wells (== test tubes).

Why 384? You could get any amount you want, you'd just have to modify the coefficients for row and column accordingly (linear increase with decrease of number per axis).

Imagine if you'd skip every other row and column, the image would still be the same, just lower resolution.

> According to what table? There is no "table below".

CTRL-F environment variables. Click on that.

>A pipette is used to dispense fluid. How does a pipette "encode position"?? Start what computation?

???

The concentrations are determined by row and column, thus encode position.

[mattkrause]

384 well plates (16x24) are one of the “standard” sizes and the densest that a typical lab is likely to have on-hand. The next size up/down (fewer, bigger wells) is probably 96 wells in an 8x12 grid.

[100ideas]

Someone should price this out on transcript aka https://strateos.com/ cloud lab...

[Apocryphon]

There was a lot of interest in this field in the late '90s over fears of Moore's Law eventually hitting a brick wall

https://en.wikipedia.org/wiki/DNA_computing

[magicalhippo]

> A pipette is used to dispense fluid. How does a pipette "encode position"??

The illustration shows this relatively clearly: at row N column M, you put N drops of solution A and M drops of solution B.

[TeMPOraL]

> A pipette is used to dispense fluid. How does a pipette "encode position"?? Start what computation?

This is shown in the picture; you put X drops of one fluid and Y drops of a different fluid, where (X, Y) is the position of a given test tube.