Skip to content

Commit

Permalink
Fix typos
Browse files Browse the repository at this point in the history
  • Loading branch information
pallada-92 authored Nov 28, 2020
1 parent d5f3894 commit cd41a11
Showing 1 changed file with 19 additions and 19 deletions.
38 changes: 19 additions & 19 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<h1 align="center">cube3d.dna</h1>

<p align="center">
Most advanced and compact 3d engine ever implemented in DNA code
The most advanced and compact 3d engine ever implemented in DNA code.
<br><br>
<img alt="environment: in vitro" src="https://img.shields.io/badge/environment-in%20vitro-red"/>
<img alt="platform: DNA | TMSD" src="https://img.shields.io/badge/platform-DNA%20%7C%20TMSD-white"/>
Expand All @@ -27,10 +27,10 @@

## How to deploy

1. Synthesise oligonucleotides from [cube3d.dna](./cube3d.dna) file.
2. Arrange test tubes as shown on the diagram below.
3. Don't forget to provide initial concentrations according to the table below.
4. Use pipette to encode position (row and column) of each tube to start computation.
1. Synthesize the oligonucleotides from the [cube3d.dna](./cube3d.dna) file.
2. Arrange the test tubes as shown in the diagram below.
3. Don't forget to provide the initial concentrations according to the table below.
4. Use a pipette to encode the position (row and column) of each tube to start the computation.

<details>
<summary>Environment variables</summary>
Expand All @@ -57,8 +57,8 @@ nz = 0.737 + -0.270 Col + 0.302 Row

## Testing

1. Pick the fluorophore of your favourite color and attach it to the `Strand R0`, so that it activates when `R` species are being produced.
2. Use the light source of specific wavelength (depending of the fluorophore you've chosen) to render the result.
1. Pick the <a href="https://en.wikipedia.org/wiki/Fluorophore">fluorophore</a> of your favorite color and attach it to the `Strand R0`, so that it activates when the `R` species are being produced.
2. Use a light source with a specific wavelength (depending on the fluorophore you've chosen) to render the result.

<p align="center">
<img src="https://hsto.org/webt/hv/q_/zy/hvq_zyw6uuwwfpg6umqthctq6tm.png" width="600"/>
Expand Down Expand Up @@ -90,62 +90,62 @@ nz = 0.737 + -0.270 Col + 0.302 Row
<tr>
<td align="center" valign="center">
<img src="https://habrastorage.org/webt/gw/zb/v1/gwzbv1w5humyabeelkyx_c3gq7k.gif" width="100%" /><br>
Simplified animation of toehold mediated strand displacement technique
Simplified animation of the toehold mediated strand displacement technique (based on supplementary materials from [2])
</td>
<td align="center" valign="center">
<img src="https://habrastorage.org/webt/ph/iv/ax/phivaxoqftqzm2h7qvbbj41dwiq.png" width="100%" /><br><br>
Types of oligonucleotides required for single reaction
The types of oligonucleotides required for a single reaction (based on supplementary materials from [2])
</td>
</tr>
<tr></tr>
<tr>
<td align="center" valign="center">
<img src="https://habrastorage.org/webt/ww/9k/xd/ww9kxd64xtigxtbpc5mm3tvsswg.png" width="100%" /><br>
Data flow graph of JS implementation
Data flow graph of the JS implementation.
</td>
<td align="center" valign="center">
<img src="https://habrastorage.org/webt/uj/_l/2_/uj_l2_q26onfetzrpq_0wfetxic.png" width="100%" /><br>
Species interaction graph of this implementation
Species interaction graph of this implementation.
</td>
</tr>
<tr></tr>
<tr>
<td align="center" valign="center">
<img src="https://habrastorage.org/webt/-j/ak/5i/-jak5iv5d7pkkosrhl_g4r3oo34.png" width="100%" /><br><br>
Unminified source code of this implementation. It is just plain reactions with a few macros.
Minifier was written in Wolfram Language specially for this project.
Unminified source code of this implementation which just comprises plain reactions with a few macros.
The minifier was written in Wolfram Language specially for this project.
</td>
<td align="center" valign="center">
<br>
<img src="https://habrastorage.org/webt/qn/-j/bu/qn-jbugqz0opyuxhvm6j09wv5te.png" width="100%" /><br><br>
CRN++ source code for comparison (CRN++ is not used in this implementation)
CRN++ source code for comparison (CRN++ is not used in this implementation).
</td>
</tr>
<tr></tr>
<tr>
<td align="center" valign="center">
<img src="https://habrastorage.org/webt/lv/ah/vs/lvahvszdgpw5vbvottwja7gwtjw.png" width="100%" /><br><br>
10 reactions after minification used in this project.
Since piperine compiler doesn't support more than 2 products in the right hand side, reactions were splitted.
10 reactions after the minification used in this project.
Since the piperine compiler doesn't support more than 2 products on the right-hand side, the reactions were split.
</td>
<td align="center" valign="center">
<br>
<img src="https://habrastorage.org/webt/lh/hx/j8/lhhxj842nxuxdocbz1zsyazvfok.png" width="100%" /><br><br>
CRN++ 70 reactions output for comparison (CRN++ is not used in this implementation)
CRN++ 70 reactions output for comparison (CRN++ is not used in this implementation).
</td>
</tr>
</table>

## Building from source

1. Install the <a href="https://github.com/DNA-and-Natural-Algorithms-Group/piperine">piperine compiler by the DNA and Natural Algorithms Group</a>.
1. Install the <a href="https://github.com/DNA-and-Natural-Algorithms-Group/piperine">piperine compiler</a> by the DNA and Natural Algorithms Group.
2. Run the following command

```
piperine-design cube3d.crn --maxspurious 0.765
```

3. Wait 2-3 hours for compilation results
3. Wait 2-3 hours for the compilation results.

## References

Expand Down

0 comments on commit cd41a11

Please sign in to comment.