Difference between revisions of "Team:NUS Singapore-A/Hardware/PDF-LA!"
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<img src="https://static.igem.org/mediawiki/2018/e/e5/T--NUS_Singapore-A--Hardware_header_C.png" class="header"> | <img src="https://static.igem.org/mediawiki/2018/e/e5/T--NUS_Singapore-A--Hardware_header_C.png" class="header"> | ||
| − | <h1> | + | <h1>P-LA! and DF-LA!</h1> |
| + | <p>Plate-Dish-Flask Light Apparatus (PDF-LA!) is a suite of three fully programmable devices compatible with standard laboratory equipment. It was used to characterize our optogenetic circuit in 12-well plates, petri dishes, and Erlenmeyer flasks.</p> | ||
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| − | + | <h2>Design - Innovation!</h2> | |
| − | <p> | + | <p>We designed PDF-LA! to help us characterize the behaviour of EL222. A research fellow sharing our lab, Dr Teh Ai Ying (Figure 1), was also interested in using our custom optogenetic tools, and so she served as our main source of user feedback throughout PDF-LA!’s design process.</p> |
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| − | < | + | <div class="quote"> This was useful to me as I needed to scale up my research. </div> |
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| − | + | <figure class="figures2" style="max-width: 60%;"> | |
| − | + | <img src="https://static.igem.org/mediawiki/2018/6/60/T--NUS_Singapore-A--Hardware_pdfla_aiying.jpg" alt="Dr Teh and her satisfaction"> | |
| − | <figure class=" | + | <figcaption><b>Figure 1</b>. Dr Teh Ai Ying, holding DF-LA!.</figcaption> |
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| − | + | <h3><i>P-LA!</i></h3> | |
| − | + | <p>The first design was a device for the 12-well plate, <i>P-LA!</i>. We designed <i>P-LA!</i> to improve on another design which had been loaned to us by a different university (Figure 2), and hence gain experience of creating custom tools for optogenetics research.</p> | |
| − | < | + | <p><i>P-LA!</i> is better than the previous design because it can accommodate 12-well plates from different manufacturers, whereas the other design could only fit a specific 12-well plate model (Figure 2). P-LA! also uses significantly less material. Fun fact: despite its name, <i>P-LA!</i> was printed with ABS filament rather than PLA filament! All our 3D-printed designs use ABS filament as it was made readily available to us by our university, and its material properties were deemed sufficient for our purposes.</p> |
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| − | <img src=" | + | <img src="https://static.igem.org/mediawiki/2018/e/e3/T--NUS_Singapore-A--Hardware_pdfla_12wellplate.png"style="display: inline-block; width: 50%;"> |
| − | + | <img src="https://static.igem.org/mediawiki/2018/5/5a/T--NUS_Singapore-A--Hardware_Peristaltic_Pump.jpeg" style="display: inline-block; width: 50%;"> | |
| − | + | <figcaption><b>Figure 2</b>. Device for 12-Well Plate a.k.a. <i>P-LA!</i> (top), previous design which cannot accommodate other models of 12-well plate (bottom).</figcaption> | |
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| − | < | + | <p>After optimizing our device for the 12-well plate, it was time to scale up and create devices for petri dishes and Erlenmeyer flasks. These two items of standard laboratory equipment were chosen based on feedback from research fellows in NUS. To provide users a more integrated solution, we produced a single device which can be used for both, <i>DF-LA!</i>. </p> |
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| − | <h3 | + | <h3><i>DF-LA!</i></h3> |
| − | + | <p>As such a device had not been designed previously, there was no existing structure to improve or draw inspiration from, and our team started from scratch. This resulted in many design iterations (Figure 13).</p> | |
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| − | + | <img src="https://static.igem.org/mediawiki/2018/3/33/T--NUS_Singapore-A--Hardware_pdfla_iteration2.gif" style="display: inline-block; width: 24%;"> | |
| − | + | <img src="https://static.igem.org/mediawiki/2018/5/5f/T--NUS_Singapore-A--Hardware_pdfla_iteration3.gif" style="display: inline-block; width: 24%;"> | |
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| − | + | <figcaption><b>Figure 3</b>. The various design iterations, starting from left. This illustrates the design features that have persisted through testing and user feedback.</figcaption> | |
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| − | < | + | <button class="accordion">First to Second Iteration</button> |
| − | < | + | <div class="panel"> |
| − | + | <p>The first iteration is for a single petri dish, which can be illuminated from top and bottom. Users wanted a system with the additional option to test two petri dishes at once, and the second iteration was conceived.</p> | |
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| − | + | <button class="accordion">Second to Third Iteration</button> | |
| − | < | + | <div class="panel"> |
| − | + | <p>The second iteration was designed such that the components to illuminate a single petri dish from the bottom could be stacked with another set of the same components to create a structure that could expose the petri dish to light from the top and bottom. This symmetry is advantageous as the functionality of a single unit doubles, and was therefore retained and developed in subsequent design iterations.</p> | |
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| − | + | <p>After that, we attempted to design a separate device for the Erlenmeyer flask, but realized that it would be much simpler and more elegant to adapt the second iteration to also accommodate the flask. The third iteration thus has an extra ring in between the devices for the petri dish. This acts as a holder for the flask. Also, the “teeth and slots” feature used to join the components together was moved from the center of the walls of the cylinder to the outer edge of the cylinder. We intended to shake the flask, and were thus concerned that the walls of the slot and the teeth would be too thin and might break due to shear stresses. We thus modified this feature for the third iteration. </p> | |
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| − | < | + | <button class="accordion">Third Iteration to Fourth Iteration</button> |
| − | < | + | <div class="panel"> |
| − | <p> | + | <p>Major changes from the third iteration to the fourth iteration are the increase in the height of the flask adapter so that the flask could also be illuminated from both top and bottom, the increase in the number of LEDs available to illuminate the flask or dish, and modifying the shape of the electronics container so that the whole structure could be cylindrical. The reason for the last change was fivefold.</p> |
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| − | + | <li>To reduce the material expended during 3D printing </li> | |
| − | + | <li>For the device to occupy a smaller area </li> | |
| − | + | <li>For the user’s comfort during transport as the inconsistency in shape in previous iterations made the structure unwieldy to carry</li> | |
| − | + | <li>To make the design aesthetically pleasing</li> | |
| − | + | <li>Last but definitely not least, to make the design infinitely more modular as users can now continuously stack combinations of <i>D-LA!</i>, the petri dish module, and <i>F-LA!</i>, the Erlenmeyer flask module, into a single column. As the components are lightweight, structural failure is not a concern, and the number of units a user can stack is only limited by the microcontroller. Many petri dishes and flasks can be illuminated simultaneously while still occupying the same area as a single testing unit. The various possible configurations of our final iteration of <i>DF-LA!</i> can be seen on our <a href="https://2018.igem.org/Team:NUS_Singapore-A/Hardware">Hardware</a> page.</li> | |
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| − | <p> | + | <p>Dr Teh reported that the final design iteration successfully fulfilled her needs.</p> |
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| − | <h2> | + | <h2>Testing</h2> |
| + | <p> | ||
| + | We validated the functionality of this component by using it to characterize the behaviour of the EL222 protein in blue light-repressible/inducible systems. Please see our <a href="https://2018.igem.org/Team:NUS_Singapore-A/Results">Results</a> page for an example of the results you can obtain if you use <i>PDF-LA!</i> to characterize your own optogenetic circuit. | ||
| + | </p> | ||
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| − | + | <h2>Construction</h2> | |
| − | <p> | + | <p> |
| + | You know you want <i>PDF-LA!</i>, and you’ve already chosen the googly eyes you’re going to stick on it. Here’s what you need to make your own. | ||
| + | </p> | ||
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| − | < | + | <h3>Bill of Materials</h3> |
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| + | <p>As we were using PDF-LA! to characterize EL222, we bought 472 nm LEDs. You may substitute our LEDs with your own. The number of LEDs here are sufficient to build one set of P-LA! and one set of DF-LA!. Googly eyes have not been included. </p> | ||
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| − | < | + | <ul> |
| − | < | + | <li>Arduino Uno x 3</li> |
| − | < | + | <li>472 nm LED x 44</li> |
| − | </ | + | <li>LED driver TLC5940 x 3</li> |
| + | <li>0.1 uF ceramic capacitor x 3</li> | ||
| + | <li>4.7 uF electrolytic capacitor x 3</li> | ||
| + | <li>28-pin IC socket x 3</li> | ||
| + | <li>9V AC adapter x 3</li> | ||
| + | </ul> | ||
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| + | <h3>Structural Assembly</h3> | ||
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| − | <figure class=" | + | <figure class="figures2" style="max-width: 70%;"> |
| − | <img src=" | + | <img src="https://static.igem.org/mediawiki/2018/6/6e/T--NUS_Singapore-A--Hardware_pdfla_12well_reverse.gif" alt="12-well" style="display: inline-block; width:60%;"> |
| − | <figcaption><b> | + | <img src="https://static.igem.org/mediawiki/2018/d/dd/T--NUS_Singapore-A--Hardware_pdfla_iteration4_reverse.gif" alt="PDF-LA!" style="display: inline-block; width:30%;"> |
| + | <figcaption><b>Figure 4</b>. Assemblies for P-LA! (left) and DF-LA! (right)</figcaption> | ||
</figure> | </figure> | ||
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| − | <p> | + | <!-- |
| + | <p>Files for lasercutting are available in DXF format, while files for 3D printing are available in STL format. You may download them all as a ZIP file <a href="#">here</a>. | ||
| + | </p>--> | ||
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| − | < | + | <!-- |
| − | < | + | <p id="a_ref">Users reported satisfaction with the final design iteration. Please visit our <a href="https://2018.igem.org/Team:NUS_Singapore-A/Hardware" id="b_ref">Hardware</a> page for more on how we conducted user testing and learned from user feedback.</p> |
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Latest revision as of 03:56, 18 October 2018
CONNECT WITH US
P-LA! and DF-LA!
Plate-Dish-Flask Light Apparatus (PDF-LA!) is a suite of three fully programmable devices compatible with standard laboratory equipment. It was used to characterize our optogenetic circuit in 12-well plates, petri dishes, and Erlenmeyer flasks.
Design - Innovation!
We designed PDF-LA! to help us characterize the behaviour of EL222. A research fellow sharing our lab, Dr Teh Ai Ying (Figure 1), was also interested in using our custom optogenetic tools, and so she served as our main source of user feedback throughout PDF-LA!’s design process.
This was useful to me as I needed to scale up my research.
P-LA!
The first design was a device for the 12-well plate, P-LA!. We designed P-LA! to improve on another design which had been loaned to us by a different university (Figure 2), and hence gain experience of creating custom tools for optogenetics research.
P-LA! is better than the previous design because it can accommodate 12-well plates from different manufacturers, whereas the other design could only fit a specific 12-well plate model (Figure 2). P-LA! also uses significantly less material. Fun fact: despite its name, P-LA! was printed with ABS filament rather than PLA filament! All our 3D-printed designs use ABS filament as it was made readily available to us by our university, and its material properties were deemed sufficient for our purposes.
After optimizing our device for the 12-well plate, it was time to scale up and create devices for petri dishes and Erlenmeyer flasks. These two items of standard laboratory equipment were chosen based on feedback from research fellows in NUS. To provide users a more integrated solution, we produced a single device which can be used for both, DF-LA!.
DF-LA!
As such a device had not been designed previously, there was no existing structure to improve or draw inspiration from, and our team started from scratch. This resulted in many design iterations (Figure 13).
The first iteration is for a single petri dish, which can be illuminated from top and bottom. Users wanted a system with the additional option to test two petri dishes at once, and the second iteration was conceived.
The second iteration was designed such that the components to illuminate a single petri dish from the bottom could be stacked with another set of the same components to create a structure that could expose the petri dish to light from the top and bottom. This symmetry is advantageous as the functionality of a single unit doubles, and was therefore retained and developed in subsequent design iterations.
After that, we attempted to design a separate device for the Erlenmeyer flask, but realized that it would be much simpler and more elegant to adapt the second iteration to also accommodate the flask. The third iteration thus has an extra ring in between the devices for the petri dish. This acts as a holder for the flask. Also, the “teeth and slots” feature used to join the components together was moved from the center of the walls of the cylinder to the outer edge of the cylinder. We intended to shake the flask, and were thus concerned that the walls of the slot and the teeth would be too thin and might break due to shear stresses. We thus modified this feature for the third iteration.
Major changes from the third iteration to the fourth iteration are the increase in the height of the flask adapter so that the flask could also be illuminated from both top and bottom, the increase in the number of LEDs available to illuminate the flask or dish, and modifying the shape of the electronics container so that the whole structure could be cylindrical. The reason for the last change was fivefold.
- To reduce the material expended during 3D printing
- For the device to occupy a smaller area
- For the user’s comfort during transport as the inconsistency in shape in previous iterations made the structure unwieldy to carry
- To make the design aesthetically pleasing
- Last but definitely not least, to make the design infinitely more modular as users can now continuously stack combinations of D-LA!, the petri dish module, and F-LA!, the Erlenmeyer flask module, into a single column. As the components are lightweight, structural failure is not a concern, and the number of units a user can stack is only limited by the microcontroller. Many petri dishes and flasks can be illuminated simultaneously while still occupying the same area as a single testing unit. The various possible configurations of our final iteration of DF-LA! can be seen on our Hardware page.
Dr Teh reported that the final design iteration successfully fulfilled her needs.
Testing
We validated the functionality of this component by using it to characterize the behaviour of the EL222 protein in blue light-repressible/inducible systems. Please see our Results page for an example of the results you can obtain if you use PDF-LA! to characterize your own optogenetic circuit.
Construction
You know you want PDF-LA!, and you’ve already chosen the googly eyes you’re going to stick on it. Here’s what you need to make your own.
Bill of Materials
As we were using PDF-LA! to characterize EL222, we bought 472 nm LEDs. You may substitute our LEDs with your own. The number of LEDs here are sufficient to build one set of P-LA! and one set of DF-LA!. Googly eyes have not been included.
- Arduino Uno x 3
- 472 nm LED x 44
- LED driver TLC5940 x 3
- 0.1 uF ceramic capacitor x 3
- 4.7 uF electrolytic capacitor x 3
- 28-pin IC socket x 3
- 9V AC adapter x 3
Structural Assembly
HEAR OUR STORY
We’re using synthetic biology to change the way the world thinks and functions.
We’re a little disruptive, dangerous and maybe a tad too bold. But the world needs some shaking up every now and then, and we think we’re just the right people for that.
Together we’re going to engineer biology and create something awesome.
CONTACT US
nusigem@gmail.com21 Lower Kent Ridge Rd, Singapore 119077