Team:Aachen/iGEM and beyond
iGEM and Beyond
One more thing
IGEM encourages students to present their bold ideas to the world. But have you ever imagined how many of such innovative solutions stay unimplemented due to the lack of access to working spaces, lab equipment, or modern technology? We decided to open the door to the world of progressive biotechnology for prospective young scientists and inventors and proudly present BioAccelerator.
The BioAccelerator is a place for students from different scientific and engineering backgrounds to meet and collaborate. While the accelerator is centered around the laboratory space, it combines it with automatization technology and artificial intelligence. We encourage our teams to be at the bleeding edge of the next bio-cyber-physical systems.
In this spirit, we organized a hackathon with the iGEM Team MSP-Maastricht to develop a fast, cheap, and reliable point-of-care test system for COVID19. The hackathon spurred some teams to continue to work on their system.
The BioAccelerator is a place for students from different scientific and engineering backgrounds to meet and collaborate. While the accelerator is centered around the laboratory space, it combines it with automatization technology and artificial intelligence. We encourage our teams to be at the bleeding edge of the next bio-cyber-physical systems.
In this spirit, we organized a hackathon with the iGEM Team MSP-Maastricht to develop a fast, cheap, and reliable point-of-care test system for COVID19. The hackathon spurred some teams to continue to work on their system.
BioAccelerator
Problems of the current situation
Inspired by iGEM, we are committed to democratize synthetic biology. Typical study programs in biology and biotechnology contain around 3 to 6 months of laboratory work over the course of the whole bachelor's degree. This is not enough time to develop sufficient laboratory skills. These skills are necessary to accelerate the advent of the synthetic biology singularity. Most of the time spend in labs exclusively consists of carrying out predefined protocols and papers. While it is necessary to learn the fundamental skills of lab work, it does not equip the students with the vital skills of critically questioning the decisions of the protocols. It discourages them to creatively ponder about their problems. It also doesn’t account for the personal preferences of each student. We know from our own experience that working on a self-defined project you are passionate about, is the best way for learning and remembering. We want to give every student the opportunity to build up their own lab, to learn on their own, or to start their first real project.
Overview
The BioAccelerator gives students a place to work on their own ideas. We are cooperating with the Exzellenz Startup Center.NRW (ESC) at the RWTH Aachen University, in order to provide students with infrastructure for their projects, from start to scaleup. The BioAccelerator stands on 3 pillars. The central pillar is to provide students with basic laboratory infrastructure. The second pillar is the integration of automatization technology into biology. The third pillar is the use of artificial intelligence to analyze the data produced. Overarching is a comprehensive education, most notably in the areas of entrepreneurship and laboratory safety.
We want to combine lab space and infrastructure designed for artificial intelligence, with the proximity to a maker space for mechanical and electrical engineering. This way, students can leverage expert knowledge along the whole process of developing a SynBio project. Accompanied by boot camps in entrepreneurship it equips the participants with knowledge in developing a project, bringing it to market, and scaling it.
We want to combine lab space and infrastructure designed for artificial intelligence, with the proximity to a maker space for mechanical and electrical engineering. This way, students can leverage expert knowledge along the whole process of developing a SynBio project. Accompanied by boot camps in entrepreneurship it equips the participants with knowledge in developing a project, bringing it to market, and scaling it.
Education
The entrepreneurship research in Aachen is highly regarded in Germany and Europe. We are currently in cooperation with the institute to develop an entrepreneurship boot camp. While many scientists behave very pioneering in the research of their respective fields, there is oftentimes a reluctance towards business topics, especially entrepreneurship. We aim to dismantle this reluctance by showing scientists that the important work doesn’t stop in the lab. The most difficult challenge is to get the research out of the university for the world to benefit from. We think it is sad that a lot of research will never leave the university walls. While the boot camp puts an emphasis on practical knowledge, like pitching skills and market analysis, we think it is important to also communicate a founding spirit. The RWTH is a major entrepreneurial hub, also due to government sponsored programs.
Never the less the boot camp also focuses on topics special to the bioeconomy, e.g. longer R&D phases, more capital intensity, and ways to mitigate them. We want to excite biotech students for the possibility to change the world. The curriculum will have a clear orientation towards tackling the most relevant problems of our time.
Never the less the boot camp also focuses on topics special to the bioeconomy, e.g. longer R&D phases, more capital intensity, and ways to mitigate them. We want to excite biotech students for the possibility to change the world. The curriculum will have a clear orientation towards tackling the most relevant problems of our time.
Infrastructure
We will cooperate with the Exzellenz Startup Center.NRW of the RWTH. This grants us a multitude of advantages. First, we will reduce a significant recurring cost as we will not have to pay rent for office spaces and possibly the removeble laboratories. While this itself already is a significant benefit it also puts us into proximity to other founder’s, which will have a significant influence on the general culture for our laboratory. The Exzellenz Startup Center.NRW incorporates a maker space with machines and equipment for mechanical and electrical engineering.
Lab
Providing a safe surrounding is the most crucial part of this project. Before people can enter the laboratory and get started, they need to pass safety tests and show that they are responsible enough to work on their own. Furthermore, in cooperation with RWTH Aachen University, students will be supported by qualified and trained professionals.
But before anyone can start working in the laboratory the equipment must be purchased or produced. Buying everything for a new laboratory is a Hercules task that`s why we aim to build some machines e.g. centrifuges in cooperation with the mechanical and electrical engineering institutes of RWTH Aachen University. Using the expertise will also attract a more diverse field of young researchers and provides the opportunity for interdisciplinary research. A “minimal“ laboratory needs to contain specific equipment. It all starts with the cultivation of organisms; this requires a least two rooms or breeders for various organisms.
Quality research requires good infrastructure. In case of a BioAccelerator, this is a well equipped laboratory. Before anything else can be done, media and buffer need to be prepared, which requires chemicals and deionized water that will be provided by a Milli-G-machine. The pH can be set with the help of a pH-meter. Of course, all the media need to be without any contamination which requires autoclaving. The cultivation of organisms is the next important step in nearly every project. For cultivation, we will use breeders in which the temperature can be set to the optimal condition for the used organism. To ensure that only the desired organisms will grow the work needs to be done under a clean bench and the organisms need a space where they can be stored when they are not used, which requires different refrigerators. After cultivation, students often need to extract products from the cell. For this, we will offer a sonicator or it can be done via chemical lysis. For separation purposes, two different centrifuges will be provided. Depending on the goal of the experiment further purification of proteins or DNA will be required. For this step, the students can use gel electrophoresis and different columns to separate proteins or DNA via different properties like size, charge, or affinity. Optical conformation of the experiment's success is a crucial part, for this a fluorescence microscope delivers the best properties, also a photometer can be an extremely helpful tool if the measurement of optical density or absorbance is required. Furthermore, the laboratory needs a sufficient amount of basic laboratory equipment like spoons, pipettes, falcons, or shake flasks, just to name a few.
Additionally, to all the specific laboratory equipment, every laboratory requires rather common items which include scales for chemicals and media compounds, pots for autoclaving, heaters and dishwashers.
The most important items are the ones that ensure the safety of the students. For this purpose, safety showers, eye-showers and hoods for safe work will be installed. A list of the equipment we want to provide in the BioAccelerator can be downloaded here:
But before anyone can start working in the laboratory the equipment must be purchased or produced. Buying everything for a new laboratory is a Hercules task that`s why we aim to build some machines e.g. centrifuges in cooperation with the mechanical and electrical engineering institutes of RWTH Aachen University. Using the expertise will also attract a more diverse field of young researchers and provides the opportunity for interdisciplinary research. A “minimal“ laboratory needs to contain specific equipment. It all starts with the cultivation of organisms; this requires a least two rooms or breeders for various organisms.
Quality research requires good infrastructure. In case of a BioAccelerator, this is a well equipped laboratory. Before anything else can be done, media and buffer need to be prepared, which requires chemicals and deionized water that will be provided by a Milli-G-machine. The pH can be set with the help of a pH-meter. Of course, all the media need to be without any contamination which requires autoclaving. The cultivation of organisms is the next important step in nearly every project. For cultivation, we will use breeders in which the temperature can be set to the optimal condition for the used organism. To ensure that only the desired organisms will grow the work needs to be done under a clean bench and the organisms need a space where they can be stored when they are not used, which requires different refrigerators. After cultivation, students often need to extract products from the cell. For this, we will offer a sonicator or it can be done via chemical lysis. For separation purposes, two different centrifuges will be provided. Depending on the goal of the experiment further purification of proteins or DNA will be required. For this step, the students can use gel electrophoresis and different columns to separate proteins or DNA via different properties like size, charge, or affinity. Optical conformation of the experiment's success is a crucial part, for this a fluorescence microscope delivers the best properties, also a photometer can be an extremely helpful tool if the measurement of optical density or absorbance is required. Furthermore, the laboratory needs a sufficient amount of basic laboratory equipment like spoons, pipettes, falcons, or shake flasks, just to name a few.
Additionally, to all the specific laboratory equipment, every laboratory requires rather common items which include scales for chemicals and media compounds, pots for autoclaving, heaters and dishwashers.
The most important items are the ones that ensure the safety of the students. For this purpose, safety showers, eye-showers and hoods for safe work will be installed. A list of the equipment we want to provide in the BioAccelerator can be downloaded here:
Funding & cooperation's
The major obstacle for the BioAccelerator is getting the required funding. We will need funding for a variety of things, including the laboratory space, the equipment, and the personnel. Then we also have to find a way to fund basic chemicals and substrates for day to day operations. It also poses a difficult challenge, to determine the total amount of cost. While the initial investment is relatively simple, the recurring costs are a magnitude more difficult to estimate.
The biggest share of the cost will be for the laboratory space. This is by far the most difficult to estimate. If we would have to acquire a laboratory building on our own, it will definitely go beyond the scope of one iGEM team. If the building would be provided, we would have two options. The first is to go the standard way and meet up with a service company to build the lab for us. Thankfully we are receiving help from the Head of Infrastructure at the IBG-1 from the FZ Jülich. We are currently preparing all the necessary facts and documents to reduce the cost of a service company. The other way is to build a removable laboratory. We inquired a first assessment of all the necessary regulatory requirements of the construction of a lab. The main ones are the “Gentechnikgesetz” and the “Biostoffverordnung”. We are currently in contact with the relevant institutes of the RWTH to write out bachelor and master theses to design a cost-effective and removable lab. The biggest challenges will be ventilation as well as the storage of gases. Never the less there is initial interest from some PhD-students to sponsor the theses with us. This way, we are honoring our philosophy and the lab will truly be from students for students. Another possibility we are currently pursuing is to get access to the practice laboratories when they are not in use. This way we can bridge many months a year.
The most immediate source of funding is the RWTH itself. This path will be considerably difficult, as RWTH is a public institution, and acquisition of funding in the public sector is always complicated. After talking to officials from the ESC, we came to the conclusion that a successful BioAccelerator will need the firm support of the biotech group at RWTH. Therefore, we are currently initiating the talk between high-level officials between the ESC and the biotech group.
The other source of funding are governmental programs or private foundations, as well as corporations.
We are preparing proposals for major German science foundations as well as governmental funding. These vary greatly in scope. Another funding opportunity comes from corporations. We present a major benefit for corporations because we have a great filtering effect. We can signal to outsiders that our participants will not only have more laboratory experience but also possess great initiative.
We need to acquire multiple sources of funding from different stakeholders. While making it more probable to acquire enough funding, it makes the whole process a lot more challenging, given that different investors have different expectations and investment horizons.
The biggest share of the cost will be for the laboratory space. This is by far the most difficult to estimate. If we would have to acquire a laboratory building on our own, it will definitely go beyond the scope of one iGEM team. If the building would be provided, we would have two options. The first is to go the standard way and meet up with a service company to build the lab for us. Thankfully we are receiving help from the Head of Infrastructure at the IBG-1 from the FZ Jülich. We are currently preparing all the necessary facts and documents to reduce the cost of a service company. The other way is to build a removable laboratory. We inquired a first assessment of all the necessary regulatory requirements of the construction of a lab. The main ones are the “Gentechnikgesetz” and the “Biostoffverordnung”. We are currently in contact with the relevant institutes of the RWTH to write out bachelor and master theses to design a cost-effective and removable lab. The biggest challenges will be ventilation as well as the storage of gases. Never the less there is initial interest from some PhD-students to sponsor the theses with us. This way, we are honoring our philosophy and the lab will truly be from students for students. Another possibility we are currently pursuing is to get access to the practice laboratories when they are not in use. This way we can bridge many months a year.
The most immediate source of funding is the RWTH itself. This path will be considerably difficult, as RWTH is a public institution, and acquisition of funding in the public sector is always complicated. After talking to officials from the ESC, we came to the conclusion that a successful BioAccelerator will need the firm support of the biotech group at RWTH. Therefore, we are currently initiating the talk between high-level officials between the ESC and the biotech group.
The other source of funding are governmental programs or private foundations, as well as corporations.
We are preparing proposals for major German science foundations as well as governmental funding. These vary greatly in scope. Another funding opportunity comes from corporations. We present a major benefit for corporations because we have a great filtering effect. We can signal to outsiders that our participants will not only have more laboratory experience but also possess great initiative.
We need to acquire multiple sources of funding from different stakeholders. While making it more probable to acquire enough funding, it makes the whole process a lot more challenging, given that different investors have different expectations and investment horizons.
AI
Artificial intelligence will play an important role in the future development of synthetic biology. Prediction of protein structure, the function of non-coding RNA, and optimization of directed evolution are only some of the many aspects of Artificial Intelligence facilitating SynBio development. Therefore, we plan to incorporate a computing infrastructure with tools for artificial intelligence, molecular dynamics, and computational biology.
Automation
While more basic purchases have priority in the beginning, we think it's vital for the future success of the BioAccelerator to make automation an integral part of lab operations and to incorporate it into the planning of the BioAccelerator from the beginning. Here we can play to our strengths in Aachen, a leading university in engineering. We plan to include other institutes from the mechanical and electrical engineering faculties as well as issuing student theses to push the limits of lab automatization technology. This way we can blend automated systems with lab operations, enabling students to gain experience with automated science as well as interdisciplinary work. An additional benefit is that we can excite students from different majors that have no previous touchpoints with biology. This facilitates cooperation and knowledge transfer between disciplines and draws more attention to the advent of the synthetic biology revolution. A clear focus on the automation pillar will be crucial to provide low-cost technology.
Covid-19 testing device Hackathon with iGEM MSP-Maastricht
For our third meet-up with the iGEM Team MSP-Maastricht we organized a “Covid-19 Hackathon”. In the face of the current pandemic, Covid-19 left no part of all our
lives untouched. The same is true for the iGEM competition. We felt the urge to direct some of our collective abilities and ideas towards solutions for the current situation.Over the course of nine hours, we worked on developing sophisticated point-of-care microfluidic quick tests for the SARS-CoV-2. First, we had some introductory lectures on the necessary topics and backgrounds, held by some team members. We started with recapitulating the biology and genomics of the SARS-CoV-2 and looked at existing methods used in testing, from PCR to ELISA approaches. It was very important for us to focus on the feasibility and the point-of-care aspect of our concepts, to achieve quick reliable test results just from the concentration found in the spit of an infected person. Our goal was to reduce the necessary lab equipment and trained professionals needed to perform the tests, to broaden the application and simplifying the whole process. We learned to work with the free to use CAD software “Fusion360” to be able to create our microchip concepts in form of a 3D Modell. In combination with a lecture on the differential calculus and programming of electrical heating and pumping systems with “Arduino-gadgets”, we were equipped perfectly to start the brainstorming and development phase of our Hackathon. We worked in groups of three, where each team had students of different fields to enrich the creation process.
After 9 long hours, we had 5 completed concepts of novel detection mechanisms for the coronavirus that could work in a point-of-care matter. Two systems used microchips in combination with different measurement techniques for the virus’s RNA. One team developed a high-sensitivity ELISA approach to detect the virus's spike-proteins inside of a microchip. Another team used a completely different approach, incorporating a Sandwich-ELISA onto the surface of a wearable face mask. The fifth concept, created by a team with two physicists used an adsorbent capture technique inside a microchip to then detect the number of bound virus particles by surface plasmon resonance.
