For a team with the purpose of democratizing biotechnology, it seems only fair that we would also engage in an adequate commitment to education in order to reach our goal. According to Philosopher and Educator Paulo Freire (also quoted above), “Education changes people and people change the world." He believed that the lack of education not only was a direct consequence of inequalities but also contributed to perpetuating them. After all, it is from the learning process that we have the opportunity to situate ourselves in the world in a critical way in order to transform it. Therefore, we felt the need as a team to use education as a way to empower people, and we found quite a few ways to achieve that goal.
Team:Open Science Global/Education
Education & Communication
Friendly solutions for a friendly community: programming DNA with Colab Notebooks
Programming is probably one of the most biased areas of technology when it comes to people who are experts in the subject. When we think about the appearance of a person from the engineering and technology fields, we almost always visualize the same profile. We understand that to democratize biotechnology is also to change this perception since the technological improvements that emerge, as well as the problems these new technologies seek to solve, are influenced by those who are developing, testing, and modifying the innovations. The inclusion of a diversity of people in science, technology, engineering, and mathematics directly affects the way in which everyone, their needs, and their ideas, are represented in these fields.
Since Friendzymes focus a lot on SynBio, when we thought about how to provide friendly solutions that can help to, at the very least, introduce people to STEM, we did so through the lens of synthetic biology and programming. When you look at the interface of these two disciplines, you find bioinformatics. The most essential aspect of bioinformatics is the data, and exploratory analysis is one way to do that. It is with this in mind that Google Colaboratory, aka Google Colab, was created. Google Colab allows you to mix executable code and rich text in a single document, without the need to download anything to your computer; thus, it is very easy to use, even for those who don't have much knowledge of programming - which is the case for many of us, synthetic biologists.
With this information in mind, we decided to create easy-to-use tutorials for accessing our software tools - created with the purpose of making the life of a genetic circuit designer easier. Some applications that we cover are: codon optimization, searching for forbidden sequences (e.g. EcoRI binding site outside the BioBrick standard prefix and suffix), and correction of problematic sequences. We invite you to check our tutorials, as well as their descriptions, in the Software section , under "The Friendzymes Toolkit".
These tutorials can easily be downloaded, put on Google Colab, and run with ease. If you are interested, we recommend you to go through our tutorials to know and get more comfortable with the tools. Each tutorial has instructions on how to download example data. When you’re finished, feel free to use these “recipes” with your own files and sequences!
Some prior knowledge of programming is required, of course, but nothing that a basic online course of a few weeks (or even a few days) cannot solve. We have also documented some successful tests of these tutorials on the Collaboration Page as we collaborated with the iGEM Design League's UTPrimers team to help optimize their circuit design.
We hope that this material will be useful beyond Friendzymes, and that it can contribute to the development of other genetic circuits around the world!
Building biostacks around the world with the Frugal Biofoundries' Hackathon
Democratizing biotechnology is a collective act - let's do it together!
Biofoundries are important tools for large-scale biotechnological production as they are highly specified infrastructures that count with many types of equipment and resources specialized in manipulating and designing with Bioparts. Many projects suggest ways to establish, grow, and scale biofoundries, but this does not have widespread feasibility - unless you have a lot of money. With that in mind, we decided to make an event to highlight how biofoundries can be useful and how people and teams can apply this in their own projects, with a pinch of inspiration from what we're doing with Friendzymes of course! So, how do you engage with others and host an event in the second year of a global pandemic?
Bioenthusiasts, unite!
It was in partnership with Just One Giant Lab (JOGL) that we decided to hold an event that was entirely participatory - a hackathon. The Friendzymes and JOGL Hackathon was one of our biggest accomplishments as a team when it comes to bringing people together to talk about frugal biofoundries. This is among the highest-ranked events on the topic according to Google search. In this event, we aimed to bring people from different backgrounds, different corners of the world to talk about Frugal Biofoundries and their possible implementation. We charged participants to think about what problems of their reality could not only be solved with Synthetic Biology, but could also be eradicated if frugal biofoundries were common.
The premise was simple: what would a frugal biofoundry look like for your country, region, or community by targeting a local problem? Each group analyzed different aspects of the bioengineering situation in their country/community, thought about critical needs and outlined a plan on how to implement the frugal biofoundry.
We gathered together in one weekend, with over 100 people who produced 9 projects and tried to come up with a plan on how to scale up a mini biofoundry. This event consisted of people from all over the world; therefore, the event had sessions at 3 different times of the day to make it easy for everyone to attend. The propositions surpassed our initial expectations. The teams came together during the event, some formed out of previous teams, some formed by single individuals who subscribed to the event, and the results were outstanding.
A dream about education
As we gave this idea life, we knew we’d have a challenge ahead of us as frugal biofoundries are a rather new concept, and linking them to democratized biotechnology was an even bolder move. Therefore, we decided we needed to have good communication of our plan to attract lots of people to the initiative and let them know what we’re really about. We designed a brand visual identity around the concept of discovering new things with democratized biotechnology and were pretty happy with the results.
Additionally, Friendzymes had the honor of hosting 3 talks with experts in different fields of education, open to everyone who wished to attend and free of charge. We dubbed these our FrugBio talks! We also had the pleasure of speaking with Timothy Styles, who gave us a very interesting introduction to his open SynBio Software (Poly)merase and Library parser, and Sebastian Cocioba, who gave us a grand tour on the tools he builds for his Genetic Engineering plant lab and how taught us how engineering can be empowering and liberating for a Synthetic Biologist on a low budget. Later, we had Chad Childers from Opentrons who showed us how open Hardware can be great allies in the path for accessible technology and democratized knowledge. Chad’s talk was followed by Isaac Larkin, who enthusiastically talked about how Frugal Biofoundries were our best choice for mass enzyme manufacturing.
These talks were an immense success, and various teams came up with extremely creative ideas that later resulted in collaborations among them. This matches one of our original goals, not only with this Hackathon, but also as a team: To bring people from around the world together to brainstorm possible solutions to modern problems using biotechnology. Below are some solutions to local issues that the competing teams presented during the final sessions of the Hackathon.
Much of our understanding about the important parts of the project came through interacting with others who were just as passionate about biotech as we are. Also, many of the initial team members didn’t know anything about biotechnology, but conversations with Scott (our PI) helped many learn about plasmids and gene editing.
When the Frugal Science class ended, a lot of people dropped off the team due to other commitments; however, 6 members of the class continued to collaborate and built Friendzymes, which has since become a very dynamic team as more people from different communities got excited about this idea. Clearly, we needed to tackle this problem globally, instead of in a specific region.
As we thought about how to push our team to the global scale, iGEM seemed like the best platform to showcase our interests, so we joined iGEM 2021!
Pump Up Recycling
Pump UP Recycling’s goal is to increase the amount of recyclable materials by providing an enzymatic solution for organic contamination on plastic, metal, and paper wastes using synthetic biology. The product they design will be easily applied from small scale homes to large scale industries. Pump Up Recycling wants to target consumers to increase their awareness of how they can easily and positively impact the environment. Nevertheless, they are not limiting themselves to consumers, Pump Up Recycling also recognizes that the largest impact will come when everyone in the chain recognizes their importance and steps up to the challenge. In fact, Pump Up Recycling believes that by getting businesses, consumers, collectors, waste collection companies, and more, the demands of their product will increase the efficiency of the whole process will be improved and directly lead to higher recycling rates.
The Amazon Biofoundry
The Amazon Biofoundry hopes to build a biofoundry in the heart of the Amazon Rainforest to have the ability to sequence the Amazon’s microorganisms directly from environmental samples, genome mining, implement bioinformatic analysis of said samples, produce enzymes on minimal-scale bench bioreactors, and achieve a high-throughput automated characterization of said enzymes.
The Amazon Biofundry hopes to develop sustainable ways of developing bioproducts, gain access to enzymes that are not being studied, and conserve the Amazon Forest as it’s crucial to science and can benefit the local economy by developing products that would have royalties return to their region, instead of going elsewhere.
Parametric Modeller
Design open-source applications for building and/or simulating a bioreactor. Parametric Modeller is designing a bioreactor that will allow for basic fluid simulations while displaying plow patterns and other flow properties at desired locations. While this is designed to be as simple and consumer-friendly as possible, it will also allow for advanced users to adjust the code to change simulation parameters, add new features, and add new templates to the software using python.
Curupira Biofoundry
Curupira Biofoundry are proposing a biofoundry that will assist local Brazilian communities to protect and manage wildlife by speeding up the domestication of microalgae strains from Brazilian biodiversity by combining industrial expertise and feedstock availability to increase the extent of biodiversity conservation. They have selected microalgae due to its ability to recover nutrients from wastewater, high yield, and efficient carbon capture. Curupira Biofoundry will use physical and chemical methods to induce mutagenesis as well as using bioprospection and artificial selection to aid in the domestication process.
X-Zymes - - - Extremophiles-Derived Enzyme and Compound Production
X-Zymes aims to provide access for identification and production of the many extremophiles that live in or around Indonesia’s volcanoes, hot springs, and deep seas. Extremophiles can help industry, health care, and more but the lack of research on these beneficial organisms limits the benefit they are currently providing.
Due to the high costs inherent to biofoundries, X-Zymes has proposed a five (5) step plan to reach their goals as frugally as possible. This involves 1) collaborating with other groups, including other iGEM groups, who have more expertise in an area than they do, 2) finding customers and strengthening relationships with research institutions and other organizations, 3) developing a frugal biofoundry from mostly DIY tools which “will require the support from Friendzymes in developing and utilizing an opentron fluid handler”, and running the biofoundry with fully-automated and high throughput tools.
The PhAB Project - Philippine Accessible Biotech
The PhAB Project’s goal is to democratize biotech research and innovation in the Philippines. Philipian labs have been limited in their molecular biology research due to high costs of enzymes and other reagents, limited supplies of lab materials due to international suppliers, and no local and sustainable source of enzymes, which was felt during the SARS-CoV-2 pandemic.
In an attempt to help reduce or eliminate some of these blocks, the PhAB Project plans to locally produce many of the needed enzymes which are often in demand for medical and industrial applications. Additionally, they plan to develop a low-cost workflow for enzyme production and utilize available expertise and resources in partnerships with Friendzymes, Beneficial.bio, and others.
Microsafe
Microsafe aims to improve the safety of handling and transporting biological samples. They have developed a ball, about the size of your hand, that can transport various biological samples with temperature control, GPS tracking to ensure it’s where you expect it, an NFC lock to provide another level of security with end to end encryption, and an internal kill switch to sterilize/decontaminate samples in emergency situations.
OpenPETase
OpenPETase is a group dedicated to averting the plastic crisis our world is facing by focusing on Polyethylene terephthalate (PET) plastics, one of the major plastics in use today. OpenPETase has 2 phases they plan to implement. The first phase involves the total breakdown of PET plastics into CO2 because this involves no genetic modifications to Ideonella sakaiensis, a bacterium that degrades PET. The second phase is where OpenPETase will use a genetically modified PETase that will allow for the reuse of PET in future plastics, thereby producing a cycle that will stop wasted plastics from being dumped into the ocean.
By using three biofoundries in Asia, America, and Europe, OpenPETase will be able to have flexibility as they work with, develop, and produce what is legal, easiest, and most frugal for each location.
InaVation - Antimicrobial Drug Discovery Frugal Biofoundry
The InaVation team aims for two goals: to create a central database that will host the data found by other researchers and to to accelerate drug discovery by utilizing the biodiversity found in Indonesia. They plan to create a frugal modular biofoundry that will form a pipeline for antimicrobial drug discovery from Indonesia’s natural resources. After their discoveries are made, they will add their data to an open-source database, which will also allow other researchers to add their data. By so doing, the overall knowledge of the interactions between biodiversity, compounds, and health will be improved to have better healthcare for all while keeping up with the drug resistance that inevitably results from overuse of a drug.
Brazilian Symposium on Synthetic Biology
This presentation was held on July 4th. In this talk, Isaac Larkin, a founder of Friendzymes, spoke about the history and inspiration for Friendzymes, including the growth of biotechnology and its potential when to bring solutions to our world’s most urgent and modern issues. He stated that making the manufacturing of enzymes and other recombinant proteins as cheap and easy as possible could reduce the issue of inaccessible biotech. He described the main issues that arise from using E. coli for the production of recombinant proteins,, including how the expensive equipment served as a bottleneck for the accessibility of this production. Since only a handful of labs can afford the equipment, this isn’t democratized at all!
While this talk branched to many topics considered important for Friendzymes and the synbio community as a whole, its focus remained on making science accessible to everyone.
IWBDA 2021
This was a talk held on Sep 23rd by Isaac Larkin. He talked about the FreeGenes project, the Open-Source wetware Design Library, and how the Designs and off-patent/IP-free genetic parts produced under this project would be distributed through Open MTA for free. The applications for this initiative in distributed mini-biofoundries were also stated since free technology is useful when developing a small infrastructure to do synthetic biology.
The discussion was held as a session of the International Web Bio-Design Automation Consortium and gladly had the participation of Alexis Casas from the London Biofoundry and a representative of the Beckman Coulter manufacturing company who talked about their new innovation center that would support iGEM teams. Every speaker had their assigned time to talk about their projects, and with a final discussion occured at the end. The results were very enlightening for the team and left Friendzymes with many new ideas. This also supported the democratized biotechnology proposition, as it was held on virtual platforms and was free for everyone to watch.
London SynBio Network
This was a talk where our representative, Ahmed, described the project in great detail and then answered questions. The goal for this presentation was to give people an overview of the Friendzymes project, what accomplish by the democratization of the manufacturing of biological parts, and how low-cost, well-implemented frugal biofoundries can be the means of achieving this goal.
iGEM KU Leuven Dragon's Biome
In this event, held by the KU Leuven iGEM team on Sep 24, we had the opportunity to introduce the audience to our project and the idea of frugal biofoundries for the mass production of Biological parts. This resulted in future collaborations and lots of interesting and informative transactions between Friendzymes and the other teams involved.
iGEM cGEM 2021
This was a presentation held for cGEM, where our representative Ahmed explained the project and held a Q&A Session about large-scale manufacturing of enzymes and other recombinant proteins and their roles in frugal biofoundries. He also emphasized the importance of a global mobilization, not only from the Scientific side but also from the Political side, for the fight against the climate crisis.