'Color Blind'

We saw the exchange between Matt747 and Jeehjung last night in the eteRNA community forum chat area concerning color and coordinates for eteRNA designs. Both ideas complement each other and would be excellent tools.

Does color blind mode mean the ability for players to assign their own colors to current data sets? If so, team blubblub has five questions stemming from our experience with coloring nucleotides: at a minimum, will the color black be added to the current color template?; will we be given the ability to assign any color to any nucleotide (Example: guanine could be red but it could also be black, yellow or blue); will the color template be made available for both the synthesized and unsynthesized data sets?; will the expanded color template be made available for player created puzzles?; will at least one nucleotide ball template be expanded to 1024 balls to accomodate new proposed design structures?

Will the additional tools appear in any of these forms? None? Some? All?

Hi, blubblub

By color blind mode, we meant adding A,U,G,C letters to each base and some number to indicate experimental data in synthesized designs. So that people can read information directly without looking at colors : )

I think color template can be useful for personal preference - I’ll add this to potential feature list. Thanks for the idea!

Thanks Jee for your response. Based on what we are seeing, we do think the current eteRNA color template (yellow for adenine, blue for uracil, red for guanine, and green for cytosine) is inhibiting your RNA designs. But we understand priorities. We will write the software ourselves.

Hi Blubblub!

Haven’t forgot what you wrote to me about color template and RNA, just been trying to figure out my opinion. We both love colors, I like Ding’s expression: Color rage. (Ah, I misread him, he wrote color range :slight_smile: )

Couldn’t read your Google article, probably lacking a program. So I’m not sure if I understood you correct.

But anyway, here is what I think so far. I can see that more colors could be helpful in some cases. I love the new advanced mode, where the blue and yellow color is stronger or weaker depending on how likely the nucleotides are to pair up. It just seems intuitively right.

But on the longer term of EteRNA I see a place where an extra mode with more colors could be helpful. Right now I think we are on the way to discover the general and big rules in RNA design – the rules that will apply in many cases. I haven’t read much about RNA yet, but as I understand, sometimes because of a specific combination of nucleotides, something special goes on below basepairlevel. Something to do with formation and bonding. As I remember when there are around 3-4 GC-pairs or more in a row, a something happens in structure, which is what makes it hard to synthesise a design with lots of GC-pairs.

I think it could be helpful with an advanced color mode, where there are put other colors around the nucleotides (like a ring), when something unusual is going on. So we can see when and where a special structure form, break these formations if they are unwanted or move them to where we want them and maybe be able to figure out a few new rules. A number instead of a color might do the trick as well.

Good luck with your work.

Eli:

This last paragraph is what we are thinking as well.

‘I think it could be helpful with an advanced color mode, where there are put other colors around the nucleotides (like a ring), when something unusual is going on. So we can see when and where a special structure form, break these formations if they are unwanted or move them to where we want them and maybe be able to figure out a few new rules. A number instead of a color might do the trick as well.’

We were unaware the Google link wasnot working properly. That is unfortunate because we basically broke out each nucleotide into a six place base-2 system, and instead of assigning a nucleotide a color value, we assigned the base-2 value places a color.

Adenine, uracil, cytosine and guanine can be any color including black. So many patterns and relationships emerged that we were able to trace the architecture to what we think is the fractal level of RNA – before the transcription level in the Central Dogma where DNA makes RNA make Protein.

Try this link: https://picasaweb.google.com/collinsm…#

If you see a balance scale photo click on it. The 'phot album with our images will come up and the captions will explain the images and the new color template. Alot of stuff you are seeing and intuiting (we believe correctly) fits well with what we can see mathematically.

If you could let us know if this link does not work we would appreciate.

Best regards,
blub blub