Difference between revisions of "Team:Madrid-OLM/HardawareMicrofluidics"

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         <title>Microfluidics part of the device</title>
 
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                             <h1 id="Teamtittle">Microfluidics</h1>
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                             <p class="lead">When the need of moving microvolumes arise as a mandatory requirement of design, microfluidics pops up as the one and only solution. Although there is at hand a wide range of microfluidic commercial solutions, many of them are too expensive to start experimenting with. </p>
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                             <p class="lead">That is why our method comes to give an alternative solution. The <a href="http://www.elveflow.com/microfluidic-tutorials/microfluidic-reviews-and-tutorials/the-poly-di-methyl-siloxane-pdms-and-microfluidics/">PDMS</a> manufacturing reveals itself as a tough rival with respect to other alternatives. PDMS was our initial choice, due to its reasonable price and ease of use. As DIY and digital manufacturing constitute the basis of our hardware, we built a workflow around the PDMS chip</p>
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                             <h2>Apartado 1</h2>
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                             <h2>Hardware</h2>
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                             <p class="lead">
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                             <p class="lead">The hardware is mainly composed of different modules, interconnected for two main purposes: distributing the powers rails through all the modules and communicating each module with the main controller.</p>
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                                Cosas del apartado 1, se necesita meter mas divs seguramente
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                            <img class= "figureimage" alt="Figure1" src="https://static.igem.org/mediawiki/2018/1/10/T--Madrid-OLM--Device--FinalPrototype--BSA.png" style="width:70%;"/>
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                             </p>
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                            <p class="lead" style="margin-left:15%; margin-right:10%;">Figure 1: Diagram of the different platforms that run the system.</p>
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                            <p class="lead">Broadly the system is composed of four main sections: </p>
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                            <ol class="ourlist">
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                                <li><p class="lead">A pump system on a microlitre scale. Composed of eight stepper motors, controlling the syringe’s pumps. It is in charge of injecting and removing the fluid from the chips. This system is directly connected to a 12V power supply and controlled through the digital pins from the main controller, Arduino Mega.</p></li>
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                                <li><p class="lead">A potentiostatic measurement system, the <a href="http://iorodeo.com/products/potentiostat-shield">Rodeostat</a>, directly connected to the microfluidic chip. It connects directly to the Arduino (Which governs the device) through Serial communication. For that purpose, the pins 26 and 31 of the P14 connector in the RodeoStat have been connected to the RX2 and TX2 pins on the Arduino Mega. The system is supplied by the 5V pin of the Arduino Mega power converter. For a more detailed description of the system, connection checks <a href="http://forum.iorodeo.com/topic/91/arduino-communication/17">this</a> threat where we have explained to the RodeoStat community our set up.</p></li>
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                                <li><p class="lead">A WiFi module, designed and developed by ourselves. The system is based on the board ESP8266, broadly extended in IoT applications. It communicates to Arduino through Serial protocol through its RX3 and TX3 pins. The purpose of this module is to uploads the data sent by Arduino to an external cloud server on FireBase. You could go over all the schematic and board designs on <a href="https://github.com/OpenLabMadrid/iGEM-Madrid-OLM/tree/master/Electronics/Final%20version/WiFi%20Module">our GitHub.</a></p></li>
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                             </ol>
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                            <h4>Foto placa wifi</h4>
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                            <p class="lead">The main controller which operates the rest of the components, Arduino Mega 2560.</p>
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                            <p class="lead nomargin"><spam class="red">CAUTION</spam>: The controllers has several modifications that allow it to work in the device. Trying to replicate it without the modifications is dangerous and can imply the universe destruction:</p>
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                            <ol class="ourlist">
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                                <li class="nomargin"><p class="lead">Arduino’s M7 diode, which job is to avoid an eventual situation of reverse current, has been removed. This is because of his inability to stand the 4 amperes that go through the system when the 8 motors are at their full capacity. In its position, we have solder a IRLZ44N transistor, able to stand up to 50 A. To do it, the pins of the source and drain were connected in a similar way as the pins of the diode and the gate pin was connected to the 12V  power supply. A heat sink was also put in the upper side.</p></li>
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                                <li><p class="lead">An Arduino Shield was mounted to increase the total of pins to 8 Vin an 8 GND, to connects the power of the motor drivers.</p></li>
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                            </ol>
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                            <h4>Foto Arduino</h4>
 
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                             <h2>Attendance to Meet Ups</h2>
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                             <h2>Software</h2>
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                             <p class="lead">The meets ups bring several advantages to the teams. It is one of the simplest ways to reach a greater number of people to whom you can explain your project. And therefore they allow you to know first-hand the projects of the rest of the teams so that you can consult and clarify doubts. These meetings also allow for more related and powerful collaborations thanks to knowing the rest of the teams in person. And last but not least, they allow you to practice exposing your project with a view to improving in the Giant Jamboree.</p>
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                             <p class="lead">As we have introduced in the previous section, our system is like a patchwork, with several different platforms including actuators, sensors and control elements.</p>
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                             <p class="lead">Our team attended two meet ups that took place in the month of August.</p>
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                             <p class="lead">Although is essential to correctly choose the programming language for the different platforms, it is mandatory to keep an eye choosing the communication protocols between all of the device’s platforms.</p>
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                             <img class= "figureimage" alt="Figure1" src="https://static.igem.org/mediawiki/2018/9/96/T--Madrid-OLM--Device--FinalPrototype--SoftwareProto.png" style="width:90%;"/>
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                            <p class="lead" style="margin-left:5%; margin-right:5%;">Figure 3: The platform’s programming languages employed and the communication protocols between all of them.</p>
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                            <p class="lead">In our circuit there are five platforms liable to be programmed:</p>
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                                <li><p class="lead">The <b>ESP8266</b>, module in charge of all the wifi communications. We have kept the original firmware because we didn’t have time to reprogramme it during this call.</p></li>
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                                            <span class="h5">Marseille</span>
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                                <li><p class="lead">In the <b>Rodeostat</b>, potentiostat responsible of the electrochemical measurements of the sensor, we modify the original firmware so it could be controlled through the Arduino Mega, instead of a computer.</p></li>
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                                <li><p class="lead">The <b>Arduino Mega</b> controls all the device, handling the motors, receiving the Rodeostat measurements and sending them to the cloud through the WiFi module or the serial communication with the PC.</p></li>
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                                <li><p class="lead">Outside the device, the data go to <b>Firebase server</b>. The server, on one hand, gets all the data and send them to an <b>iOS design app</b>, where the final user can watch the development of the data in real time.</p></li>
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                                            <h3>Mediterranean Meet Up (Marseille)</h3>
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                                <li><p class="lead">Finally, a <b>PC program</b>, written in python with Qt creator, is able to communicate through the serial protocol with the device. The application let you configure 8 different motors, run protocols sequentially or inject liquid in the microfluidic chips.</p></li>
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                            </ol>
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                                            <p class="lead">This meet up took place between Thursday 9 and Friday 10 August in the city of Marseille and was organized by the team of this city, the Aix-Marseille. In it, all the teams from the Mediterranean area were summoned, so they ended up attending both France and Spain. Francisco, Gonzalo and Ivan attended this meet up on behalf of the team.</p>
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                            <img class= "figureimage" alt="Figure1" src="https://static.igem.org/mediawiki/2018/6/62/T--Madrid-OLM--Device--FinalPrototype--CapturProgram.png" style="width:80%;"/>
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                                            <p class="lead">The event began with a reception in which all teams had their first informal contact. Subsequently, a 5 minutes presentation of each of the projects was organized, summarizing the concept on which the proyect was based, the work carried out and the plans to complete it. After the exhibition, each team answered the questions that could have the jury and the rest of the teams.</p>
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                            <p class="lead">You can find the code for the PC app, the Arduino control and the Rodeostat’s modified firmware in <a href="http://github.com/OpenLabMadrid/iGEM-Madrid-OLM">our GitHub.</a> Both the iOS app and the firebase server was set up thanks to the help of <b>Marcos Hernández Cifuentes</b>.</p>
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                                            <p class="lead">Later they invited us to a joint meal. In the afternoon it was organized a sightseeing tour of the city, but due to inclement weather it had to be suspended, although we could enjoy a pleasant evening of board games and conversations with the rest of the teams. At night a meeting was also organized in a pub to end a day where we had met many new people.</p>
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                                            <p class="lead">The second (and last day) had two interesting activities. The first was the meetings with different experts from the university, which privately asked each team about controversial issues. To see if these issues had been taken into account and the possible solutions and consequences were debated.</p>
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                                            <p class="lead">To close the event, a poster presentation session was held, which was very enriching to know how to present our project in Boston..</p>
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                                            <p class="lead">One of the things that were achieved in this meet up was the agreement with the UPF-CRG-Barcelona group to organize an activity in their meet up. Activity that is explained in the following session (and that gave rise to a greater collaboration).</p>
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                                            <span class="h5">Barcelona</span>
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                                            <h3>Spanish Meet Up (Barcelona)</h3>
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                                            <p class="lead">This meet up took place between Saturday 18 and Monday 20 August in the city of Barcelona and was organized by one of the two teams of this same city, the UPF-CRG-Barcelona. In it, all the teams from Spain were called, which all but the Valencia team attended. To this meet up they were representing the whole team: Laura, Iván and Francisco. The meet up took place in the Biomedical Research Park of Barcelona (PRBB), center where the host team operates and where they started with a welcome activity. This activity consisted of a game where each one of the assistants of each team presented themselves, so that the subsequent environment was much more relaxed.</p>
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                                            <p class="lead">The next activity was the one organized by our team. In this activity we proposed to carry out a collaborative guide in which each group would give the main ideas on how they have solved the main problems that have arisen in iGEM. The structure we proposed was followed. We collected these ideas and wrote a complete guide. We explain this collaboration in a later section of the collaborations. After this, some playful activities were carried out on the beach, including volleyball games. </p>
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                                            <p class="lead">During the morning of the second day, a more detailed presentation of each team's project was made. There was 30 minutes to expose each project in detail. This activity was very useful because the rest of the teams, besides getting to know the details of each project well, could intervene to give advice on how to make the presentations. Each team took a series of points in which they could be reinforced in the face of the presentation of the Giant Jamboree.</p>
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                                            <p class="lead">In the afternoon the time was taken to take a tour in the tourist center of the city and ended up having dinner with a picnic in the Parc Guell. A viewpoint that have views of the entire city at night.</p>
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                                            <p class="lead">During the morning of the last day, to close the meet up, we were able to attend to some enriching expert talks. They offered us their views on synthetic biology and they explained the works in which they are immersed today.</p>
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                            <h2>Organization of a Meet Up: Another European Meet Up</h2>
 
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                            <h5>Reason</h5>
 
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                            <p class="lead">After attending two meet ups we realized that these meetings are very enriching experiences in preparation for the Giant Jamboree. One of the main reasons for these meet ups is to get to know and know the project of other teams. Other reason is that its also serves to practice the presentations of the project and its results. And finally serve to open the network of contacts beyond the contest itself.</p>
 
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                            <p class="lead">We realized that the events to which more teams come are usually the first ones to be organized, and in these although if they serve to obtain collaborations, do not fulfill so much the function of practicing to present the results of your project due to at the beginning of the summer there are no results.</p>
 
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                            <p class="lead">This year the European meet up was on July 20. Date in which novice teams, without sufficient contacts do not yet know how to deal with these events and do not have the necessary funds to attend. And teams with more experience do not yet have conclusive results. With this context we proposed this ambitious project: Make another European meet up. We invited all the teams of the continent in mid-September. A date that was supposed to be the best for the organization of new teams and with the possibility of simulating the final event.</p>
 
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                            <h5>Event</h5>
 
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                            <p class="lead">The event was organized between September 14 and 16. Although this event was given as much publicity as possible and contact was made with all possible teams in Europe, attendance was low due to several factors:</p>
 
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                                <li>
 
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                                    <p class="lead"><b>- Spain is geographically at one end of Europe and travel is expensive.</b></p>     
 
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                                <li>
 
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                                    <p class="lead"><b>- The teams were short of funds and were saving for the trip to Boston.</b></p>
 
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                                <li>
 
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                                    <p class="lead"><b>- The event was announced at the beginning of September, many teams did not have room to maneuver in their organization to attend.</b></p>     
 
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                                </li>
 
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                            </ul>
 
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                            <br/>
 
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                            <p class="lead">Despite these inconveniences we had assistance from several participants of some teams (all of them came from within the Spanish territory thanks to the facilities for transport). Although there was an extensive program of activities, these had to be adjusted and reorganized so that the maximum number of attendees could enjoy them.</p>
 
−
                       
 
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                            <h5>Activities</h5>
 
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                            <p class="lead">The event began on Friday the 14th in the afternoon with the main course. In it, after the reception of the attendees we gave way to a series of very interesting expert presentations. We were able to count on the attendance of the following personalities</p>
 
−
                            <p class="lead"><u><b>Victor de Lorenzo</b></u></p>
 
−
                            <p class="lead">He is one of the Spanish most relevant researchers in the Synthetic Biology field. He work in the National Biotechnology Center (CNB) a part of the Superior Council of Scientific Investigations (CSIC). His laboratory is specialized in solving environmental issues using genetically engineered Pseudomonas putida. He gave us an interesting talk about <i>"Synthetic Biology in the rescue of the planet Earth"</i>.</p>
 
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                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/e/ee/T--Madrid-OLM--Collaboration--Madrid--Conference1.png" style="width:70%;"/>
 
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                            <p class="lead"><u><b>Saul Ares</b></u></p>
 
−
                            <p class="lead">He is a researcher of the CNB too. His work is central in the mathematical modeling of Synthetic Biology systems. He has also collaborated with previous iGEM teams. His presentation talked about <i>"How do cyanobacteria count to ten"</i>.</p>
 
−
                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/7/7e/T--Madrid-OLM--Collaboration--Madrid--Conference2.png" style="width:70%;"/>
 
−
                           
 
−
                            <p class="lead"><u><b>Krzysztof Wabnik</b></u></p>
 
−
                            <p class="lead">He is a Young Investigator Researcher of the Center for Biotechnology and Plant Genomics (CBGP) at the Polytechnic University of Madrid (UPM). The group he is leading uses multilevel computer model simulations, synthetic biology experiments and microfluidics. The name of his presentation was: <i>"Combining computational and synthetic biology approaches to understand the dynamics of plant hormone signaling circuits"</i>.</p>
 
−
                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/2/2d/T--Madrid-OLM--Collaboration--Madrid--Conference3.png" style="width:70%;"/>
 
−
                           
 
−
                            <p class="lead">Despite these inconveniences we had assistance from several participants of some teams (all of them came from within the Spanish territory thanks to the facilities for transport). Although there was an extensive program of activities, these had to be adjusted and reorganized so that the maximum number of attendees could enjoy them.</p>
 
−
                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/4/4a/T--Madrid-OLM--Collaboration--Madrid--Conference4.png" style="width:70%;"/>
 
−
                            <p class="lead">After the talks a social event was held in which the attending teams could relax having dinner in the center of Madrid with one of the most typical activities here: go out for tapas.</p>
 
−
                            <p class="lead">The second day was inaugurated with a visit to the university to show the facilities where our team works and it was explained which procedures are used in each of the sections that were visited.</p>
 
−
                            <p class="lead">Subsequently, the presentations of the projects were made. A simulation of the presentation was carried out as it should be done in Boston, to learn how to take the time and try to correct the excesses or lack of time in each section that was exposed.</p>
 
−
                            <p class="lead">In the afternoon there was a tour around Madrid, where the most iconic places of the city were shown. And although there were activities scheduled for the next day, this was the activity that closed the meet up, since the attending teams had organized to return to their cities after this tour.</p>
 
−
                            <img alt="Image5" src="https://static.igem.org/mediawiki/2018/3/30/T--Madrid-OLM--Collaboration--Madrid--Tour.png" style="width:70%;"/>
 
−
                            <h5>Conclusion</h5>
 
−
                            <p class="lead">It was an event that few people could attend, due to the conditions explained above, but from which the attendees took much advantage. Holding such an event in September could be much more crowded if it was announced from the beginning of the summer and allowed the rest of the teams to organize around it. As it provides a series of very useful tools for the presentation of Boston.</p>
 
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Revision as of 09:49, 15 October 2018

Madrid-OLM

Microfluidics part of the device

Microfluidics

When the need of moving microvolumes arise as a mandatory requirement of design, microfluidics pops up as the one and only solution. Although there is at hand a wide range of microfluidic commercial solutions, many of them are too expensive to start experimenting with.

That is why our method comes to give an alternative solution. The PDMS manufacturing reveals itself as a tough rival with respect to other alternatives. PDMS was our initial choice, due to its reasonable price and ease of use. As DIY and digital manufacturing constitute the basis of our hardware, we built a workflow around the PDMS chip

Hardware

The hardware is mainly composed of different modules, interconnected for two main purposes: distributing the powers rails through all the modules and communicating each module with the main controller.

Figure1

Figure 1: Diagram of the different platforms that run the system.

Broadly the system is composed of four main sections:

  1. A pump system on a microlitre scale. Composed of eight stepper motors, controlling the syringe’s pumps. It is in charge of injecting and removing the fluid from the chips. This system is directly connected to a 12V power supply and controlled through the digital pins from the main controller, Arduino Mega.

  2. A potentiostatic measurement system, the Rodeostat, directly connected to the microfluidic chip. It connects directly to the Arduino (Which governs the device) through Serial communication. For that purpose, the pins 26 and 31 of the P14 connector in the RodeoStat have been connected to the RX2 and TX2 pins on the Arduino Mega. The system is supplied by the 5V pin of the Arduino Mega power converter. For a more detailed description of the system, connection checks this threat where we have explained to the RodeoStat community our set up.

  3. A WiFi module, designed and developed by ourselves. The system is based on the board ESP8266, broadly extended in IoT applications. It communicates to Arduino through Serial protocol through its RX3 and TX3 pins. The purpose of this module is to uploads the data sent by Arduino to an external cloud server on FireBase. You could go over all the schematic and board designs on our GitHub.

Foto placa wifi

The main controller which operates the rest of the components, Arduino Mega 2560.

CAUTION: The controllers has several modifications that allow it to work in the device. Trying to replicate it without the modifications is dangerous and can imply the universe destruction:

  1. Arduino’s M7 diode, which job is to avoid an eventual situation of reverse current, has been removed. This is because of his inability to stand the 4 amperes that go through the system when the 8 motors are at their full capacity. In its position, we have solder a IRLZ44N transistor, able to stand up to 50 A. To do it, the pins of the source and drain were connected in a similar way as the pins of the diode and the gate pin was connected to the 12V power supply. A heat sink was also put in the upper side.

  2. An Arduino Shield was mounted to increase the total of pins to 8 Vin an 8 GND, to connects the power of the motor drivers.

Foto Arduino

Software

As we have introduced in the previous section, our system is like a patchwork, with several different platforms including actuators, sensors and control elements.

Although is essential to correctly choose the programming language for the different platforms, it is mandatory to keep an eye choosing the communication protocols between all of the device’s platforms.

Figure1

Figure 3: The platform’s programming languages employed and the communication protocols between all of them.

In our circuit there are five platforms liable to be programmed:

  1. The ESP8266, module in charge of all the wifi communications. We have kept the original firmware because we didn’t have time to reprogramme it during this call.

  2. In the Rodeostat, potentiostat responsible of the electrochemical measurements of the sensor, we modify the original firmware so it could be controlled through the Arduino Mega, instead of a computer.

  3. The Arduino Mega controls all the device, handling the motors, receiving the Rodeostat measurements and sending them to the cloud through the WiFi module or the serial communication with the PC.

  4. Outside the device, the data go to Firebase server. The server, on one hand, gets all the data and send them to an iOS design app, where the final user can watch the development of the data in real time.

  5. Finally, a PC program, written in python with Qt creator, is able to communicate through the serial protocol with the device. The application let you configure 8 different motors, run protocols sequentially or inject liquid in the microfluidic chips.

Figure1

You can find the code for the PC app, the Arduino control and the Rodeostat’s modified firmware in our GitHub. Both the iOS app and the firebase server was set up thanks to the help of Marcos Hernández Cifuentes.