Difference between revisions of "Team:IISc-Bangalore/Hardware/Notebook"
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<div id="inPageNav"> | <div id="inPageNav"> | ||
<ol> | <ol> | ||
| − | <li> | + | <li><a href="#gc">Growth Curves</a></li> |
| − | <li> | + | <li><a href="#box">Box</a></li> |
| − | <li> | + | <li><a href="#3d">3D</a></li> |
| − | <li> | + | <li><a href="#yeast">Yeast</a></li> |
| + | <li><a href="#pro">Pro</a></li> | ||
| + | <li><a href="#7way">7-Way Connector</a></li> | ||
| + | <li><a href="#mul">Multiplexing</a></li> | ||
| + | <li><a href="#cd">Current Drift</a></li> | ||
| + | <li><a href="#calibration">Calibration</a></li> | ||
| + | <li><a href="#ping">Ping!</a></li> | ||
| + | <li><a href="#pump">Pump</a></li> | ||
| + | <li><a href="#needle">Needle</a></li> | ||
| + | <li><a href="#extend">Extend</a></li> | ||
| + | <li><a href="#wf">Way Forward</a></li> | ||
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</ol> | </ol> | ||
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This page illustrates how our designs and ideas evolved over the course of the months we spent working on GCODe. We used the resources of the Indian Institute of Science, setting up our device in bio labs, talking to biology professors and instructors, who gave us some wonderful feedback and ideas, as you will see | This page illustrates how our designs and ideas evolved over the course of the months we spent working on GCODe. We used the resources of the Indian Institute of Science, setting up our device in bio labs, talking to biology professors and instructors, who gave us some wonderful feedback and ideas, as you will see | ||
| − | Growth Curves | + | <h2 id = "gc">Growth Curves</h2> |
We discover the pain of running growth curves, over and over. | We discover the pain of running growth curves, over and over. | ||
| − | Box | + | |
| + | <h2 id = "box">Box</h2> | ||
<p>It is settled. Our hardware team decides to build an automated optical density meter. Arguments reign over whether it should be a cylinder or a cuboid. Cuboid wins because it is easier to make out of a flat sheet of acrylic.</p> | <p>It is settled. Our hardware team decides to build an automated optical density meter. Arguments reign over whether it should be a cylinder or a cuboid. Cuboid wins because it is easier to make out of a flat sheet of acrylic.</p> | ||
| − | <img src="https://static.igem.org/mediawiki/2017/ | + | <img src="https://static.igem.org/mediawiki/2017/e/e6/T--IISc-Bangalore--HW-Notebook-case3ppl.jpg" align ="center" height = "400"> |
| + | |||
| − | + | <h2 id = "3d">3-D</h2> | |
All gung-ho, we print a test tube holder at the Centre for Product Design and Manufacturing, at (relatively) great expense. Mr. Srinivasan from CPDM points out we don’t need it and there are simpler ways to hold the LED in place. We switch to laser cutting everything: the device becomes much cheaper and more accessible. | All gung-ho, we print a test tube holder at the Centre for Product Design and Manufacturing, at (relatively) great expense. Mr. Srinivasan from CPDM points out we don’t need it and there are simpler ways to hold the LED in place. We switch to laser cutting everything: the device becomes much cheaper and more accessible. | ||
<img src="https://static.igem.org/mediawiki/2017/a/a6/T--IISc-Bangalore--HW-Notebook-3d-holder.png" align ="center" height = "400"> | <img src="https://static.igem.org/mediawiki/2017/a/a6/T--IISc-Bangalore--HW-Notebook-3d-holder.png" align ="center" height = "400"> | ||
| − | Yeast | + | |
| + | <h2 id = "yeast">Yeast</h2> | ||
The iGEM wet lab team at this point is working on yeast, which grows to very high ODs, which can’t be measured directly. They point out to us that automatic dilution will be a very useful feature. We agree. | The iGEM wet lab team at this point is working on yeast, which grows to very high ODs, which can’t be measured directly. They point out to us that automatic dilution will be a very useful feature. We agree. | ||
| − | Pro | + | |
| + | <h2 id = "pro">Pro</h2> | ||
Plans are made for versions going all the way up to 4, including adding all sorts of chemical reagents and measuring everything under the sun. Reality sets in. Version 2 becomes the Pro | Plans are made for versions going all the way up to 4, including adding all sorts of chemical reagents and measuring everything under the sun. Reality sets in. Version 2 becomes the Pro | ||
| − | 7- | + | |
| + | <h2 id = "7way">7-Way Connector</h2> | ||
Undergraduate Biology instructor T. Srinath points out that we need to maintain sterility and not let the pipes get clogged with stray cells. We decide to flush the system with ethanol. Our beautiful 7-way 3d printed tube connector has to be junked, because the ABS plastic is not ethanol-compatible. We switch to using medical tubing connectors since they are already biocompatible. | Undergraduate Biology instructor T. Srinath points out that we need to maintain sterility and not let the pipes get clogged with stray cells. We decide to flush the system with ethanol. Our beautiful 7-way 3d printed tube connector has to be junked, because the ABS plastic is not ethanol-compatible. We switch to using medical tubing connectors since they are already biocompatible. | ||
<img src="https://static.igem.org/mediawiki/2017/3/36/T--IISc-Bangalore--HW-Notebook-7way.png" align ="center" height = "400"> | <img src="https://static.igem.org/mediawiki/2017/3/36/T--IISc-Bangalore--HW-Notebook-7way.png" align ="center" height = "400"> | ||
| − | Multiplexing | + | <h2 id = "mul">Multiplexing</h2> |
Oh the horror of trying to close off pipes with cheap little motors! First we try pinching them shut. Then we try kinking them shut with a revolver barrel-like cylinder. Turns out with great style comes great friction. The reason it’s so hard is that we are trying to multiplex all the pipes in one place, so we can cut costs by using only one peristaltic pump. Eventually we decide to use separate servos and stopcocks to close off each pipe. This makes it easy to control each pipe electronically. | Oh the horror of trying to close off pipes with cheap little motors! First we try pinching them shut. Then we try kinking them shut with a revolver barrel-like cylinder. Turns out with great style comes great friction. The reason it’s so hard is that we are trying to multiplex all the pipes in one place, so we can cut costs by using only one peristaltic pump. Eventually we decide to use separate servos and stopcocks to close off each pipe. This makes it easy to control each pipe electronically. | ||
<img src="https://static.igem.org/mediawiki/2017/6/6c/T--IISc-Bangalore--HW-Notebook-Pratyushawithpinchythingy.jpg" align ="center" height = "400"> | <img src="https://static.igem.org/mediawiki/2017/6/6c/T--IISc-Bangalore--HW-Notebook-Pratyushawithpinchythingy.jpg" align ="center" height = "400"> | ||
| − | Current Drift | + | |
| + | <h2 id = "cd">Current Drift</h2> | ||
Professor Rajan from Electronics points out we need a current driver for our LED. This immediately fixes the horrible fluctuations in readings which threatened to sink our project. | Professor Rajan from Electronics points out we need a current driver for our LED. This immediately fixes the horrible fluctuations in readings which threatened to sink our project. | ||
| − | Calibration | + | |
| + | <h2 id = "calibration">Calibration</h2> | ||
Professor Sai Siva Gorthi of the Optics and Microfluidics Lab assuages our worries about the OD not matching the spectrophotometer by pointing out that our optical parameters are different (in Beer-Lambert’s Law), so all we need is for our reading to be proportional. | Professor Sai Siva Gorthi of the Optics and Microfluidics Lab assuages our worries about the OD not matching the spectrophotometer by pointing out that our optical parameters are different (in Beer-Lambert’s Law), so all we need is for our reading to be proportional. | ||
| − | Ping! | + | |
| + | <h2 id = "ping">Ping!</h2> | ||
GUI made! The Mini is finally usable by biologists! Srinath suggests sending a notification to your phone when the OD reaches the desired level - a brilliant idea! We immediately implement this using Pushbullet. | GUI made! The Mini is finally usable by biologists! Srinath suggests sending a notification to your phone when the OD reaches the desired level - a brilliant idea! We immediately implement this using Pushbullet. | ||
| − | + | <img src="https://static.igem.org/mediawiki/2017/2/23/T--IISc-Bangalore--HW-Notebook-pushb.jpg" align ="center" height = "400"> | |
| − | Pump | + | |
| + | <h2 id = "pump">Pump</h2> | ||
A flow cytometry instructor reminds us that the peristaltic pump is volumetric, so we can simply run the pump for a set time interval to dilute our sample with an exact quantity of water - this is great news! | A flow cytometry instructor reminds us that the peristaltic pump is volumetric, so we can simply run the pump for a set time interval to dilute our sample with an exact quantity of water - this is great news! | ||
| − | Needle | + | |
| + | <h2 id = "needle">Needle</h2> | ||
We consider using fancy and really expensive cuvettes with pipe fittings to hold our sample in front of the LED and carry it away. Dr. Moumita Koley from the Chemistry Department suggests we simply use a needle and syringe to fill the cuvette! We save hours of work, and hundreds of dollars, at the cost of some embarassment that we didn’t think of it ourselves. | We consider using fancy and really expensive cuvettes with pipe fittings to hold our sample in front of the LED and carry it away. Dr. Moumita Koley from the Chemistry Department suggests we simply use a needle and syringe to fill the cuvette! We save hours of work, and hundreds of dollars, at the cost of some embarassment that we didn’t think of it ourselves. | ||
| − | Extend | + | |
| + | <h2 id = "extend">Extend</h2> | ||
Dr. Neha Bahl, Undergraduate biology instructor, asks for a simple and immensely useful feature: the ability to to extend the growth curve at the press of a button after viewing the real-time graph on her phone. We implement it pronto. | Dr. Neha Bahl, Undergraduate biology instructor, asks for a simple and immensely useful feature: the ability to to extend the growth curve at the press of a button after viewing the real-time graph on her phone. We implement it pronto. | ||
| − | |||
| − | |||
| + | <h2 id = "wf">Way Forward</h2> | ||
| + | Dr. Neha Bahl, Undergraduate biology instructor points out the utility of a version with two test tube slots, so that comparisons can be run automatically. Professor Sai Siva Gorthi suggests implementing different wavelengths so that we can run GCODe for longer without the optical density saturating. We don’t have time to implement these ideas before the Jamboree, but just you wait! | ||
| − | <p | + | <p>Oh, you don't want to wait? Want to build your own? Head over to <a href="https://2017.igem.org/Team:IISc-Bangalore/Hardware/Documentation">Build Your Own</a> for all the gory details on how to build, set up and calibrate your very own GCODe Pro or Mini!</p> |
| − | |||
</div> | </div> | ||
</html> | </html> | ||
Revision as of 17:12, 28 October 2017
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The Road to GCODe
This page illustrates how our designs and ideas evolved over the course of the months we spent working on GCODe. We used the resources of the Indian Institute of Science, setting up our device in bio labs, talking to biology professors and instructors, who gave us some wonderful feedback and ideas, as you will seeGrowth Curves
We discover the pain of running growth curves, over and over.Box
It is settled. Our hardware team decides to build an automated optical density meter. Arguments reign over whether it should be a cylinder or a cuboid. Cuboid wins because it is easier to make out of a flat sheet of acrylic.
3-D
All gung-ho, we print a test tube holder at the Centre for Product Design and Manufacturing, at (relatively) great expense. Mr. Srinivasan from CPDM points out we don’t need it and there are simpler ways to hold the LED in place. We switch to laser cutting everything: the device becomes much cheaper and more accessible.
Yeast
The iGEM wet lab team at this point is working on yeast, which grows to very high ODs, which can’t be measured directly. They point out to us that automatic dilution will be a very useful feature. We agree.Pro
Plans are made for versions going all the way up to 4, including adding all sorts of chemical reagents and measuring everything under the sun. Reality sets in. Version 2 becomes the Pro7-Way Connector
Undergraduate Biology instructor T. Srinath points out that we need to maintain sterility and not let the pipes get clogged with stray cells. We decide to flush the system with ethanol. Our beautiful 7-way 3d printed tube connector has to be junked, because the ABS plastic is not ethanol-compatible. We switch to using medical tubing connectors since they are already biocompatible.
Multiplexing
Oh the horror of trying to close off pipes with cheap little motors! First we try pinching them shut. Then we try kinking them shut with a revolver barrel-like cylinder. Turns out with great style comes great friction. The reason it’s so hard is that we are trying to multiplex all the pipes in one place, so we can cut costs by using only one peristaltic pump. Eventually we decide to use separate servos and stopcocks to close off each pipe. This makes it easy to control each pipe electronically.
Current Drift
Professor Rajan from Electronics points out we need a current driver for our LED. This immediately fixes the horrible fluctuations in readings which threatened to sink our project.Calibration
Professor Sai Siva Gorthi of the Optics and Microfluidics Lab assuages our worries about the OD not matching the spectrophotometer by pointing out that our optical parameters are different (in Beer-Lambert’s Law), so all we need is for our reading to be proportional.Ping!
GUI made! The Mini is finally usable by biologists! Srinath suggests sending a notification to your phone when the OD reaches the desired level - a brilliant idea! We immediately implement this using Pushbullet.
Pump
A flow cytometry instructor reminds us that the peristaltic pump is volumetric, so we can simply run the pump for a set time interval to dilute our sample with an exact quantity of water - this is great news!Needle
We consider using fancy and really expensive cuvettes with pipe fittings to hold our sample in front of the LED and carry it away. Dr. Moumita Koley from the Chemistry Department suggests we simply use a needle and syringe to fill the cuvette! We save hours of work, and hundreds of dollars, at the cost of some embarassment that we didn’t think of it ourselves.Extend
Dr. Neha Bahl, Undergraduate biology instructor, asks for a simple and immensely useful feature: the ability to to extend the growth curve at the press of a button after viewing the real-time graph on her phone. We implement it pronto.Way Forward
Dr. Neha Bahl, Undergraduate biology instructor points out the utility of a version with two test tube slots, so that comparisons can be run automatically. Professor Sai Siva Gorthi suggests implementing different wavelengths so that we can run GCODe for longer without the optical density saturating. We don’t have time to implement these ideas before the Jamboree, but just you wait!Oh, you don't want to wait? Want to build your own? Head over to Build Your Own for all the gory details on how to build, set up and calibrate your very own GCODe Pro or Mini!
