Team:Open Science Global/Human Practices/Integrated Human Practices

Integrated Human Practices

The community in motion on the advent of the Friendzymes Project: our Integrated Human Practices

The creation and shaping of the international team and the Friendzymes Project was born out of an online class with more than 400 people from around the world; this unique beginning causes Friendzymes’ Integrated Human Practices to be a little unusual when compared to many other iGEM teams.

After beginning in the class, Friendzymes has evolved into a team with people from 10 countries on 5 of the 7 continents of the world, and is constantly mixing with the knowledge and enthusiasm great researchers and bio-enthusiasts not of our team have for Synthetic Biology. Our vision is to build a frugal biofoundry, to bring the technology and application of biological sciences to the level of the community, and to make friends — as our name suggests! By working with various communities, we can achieve our vision.

Part I: The Frugal Science online class conducted by Dr. Manu Prakash

The seed of the Friendzymes Project was born in August 2020 in the Frugal Science online class taught by Bioengineering Assistant Professor Manu Prakash from Stanford University. Manu is a world-renowned, innovative scientist whose work focuses on frugal innovations to make medicine, computing, and microscopy accessible to more people across the world.

The spirit of the class was for people to come together during hopeless times, such as the pandemic, and try to look at the bigger picture, define world problems, and discuss potential solutions. This class had two parts: frugal engineering guest lecturers and group projects where students united based on similar interests. This built an international community of those wanting to tackle problems of our times. The global issue of democratizing biotechnology was raised and the solution of tackling it via enzyme production was proposed by Isaac Larkin, a team leader of the Friendzymes project.

When thinking about this issue, Isaac wondered what we would need to build in order to frugally build a bio lab. He was already working on an Open Enzyme collection for COVID diagnostics and this idea was a broader scheme of frugal biotech. The things he thought might be necessary were: “a frugal bioreactor for culturing microbes to manufacture enzymes and other biological reagents, a frugal thermocycler for copying/amplifying DNA (and incubating reactions at set temperatures); a frugal pipette to enable people to do liquid handling and set up reactions in the lab; a frugal electrophoresis apparatus aimed at measuring the weight of molecules; a frugal optical measurement device for probing the structure of molecules; a frugal French Press instrument, for popping cells and accessing their intracellular contents; a frugal centrifuge like paperfuge or handyfuge, for separating heavy/insoluble materials and liquids from less dense and soluble solutions; and at least two ideas devoted to cheap manufacturing of enzymes/biomolecular reagents required to perform biochemical/biotechnological reactions and transformations. This is a great start on a roadmap for building a frugal bio lab. To summarize, we'll need: (1) frugal ways to grow cells and make wetware/reagents, (2) frugal ways to set up reactions, (3) frugal ways to separate/concentrate/purify things, (4) frugal ways to run reactions at specific temperatures, and (5) frugal ways to measure the results of experiments, including potentially the size/structure/concentration of molecules, cells and product materials.” - Isaac L

The scope of this problem was very large and further discussions with others as a part of the class helped to prune out the unnecessary goals and focus on the most important thing, frugal bioreactors. Leron Perez, a graduate student from Stanford University, who was part of the class, strongly suggested that a frugal bioreactor will be one of the most important components in this pursuit. We explored the diverse frugal bioreactor designs and decided it would be an important component in the pipeline we would set up. For information regarding our progress on the frugal bioreactor, check out our Hardware section.

Divij Kinger, a former member of the team, is a Biotech/Genetic Engineer who was working on Gene Drives to prevent transmission of Dengue in mosquitoes, saw the need to store, transport, and use plasmids, DNAs, and enzymes as a necessary component of any biolab. He suggested that minimizing transportation barriers would help local communities in making and sharing biological constructs among themselves. Therefore, we started looking for organisms that can withstand uncertain environmental factors and can be easily shipped.

Luckily, we were able to talk to Keoni Gandall, who had a solution ready because he ran a company that specialized in creating genes and packaging them as spores to the end consumer. It seemed magical without having to deal with any storage facility where you can mail your genetic constructs because the spores can be transferred to paper. The only catch was that protein production wasn’t very abundantly done in Bacillus subtilis, the organism forming those spores. The standard was, and is, Escherichia coli because everyone has been thinking of ways to make protein production better in E. coli, instead of thinking out of the box and going with less conventional model organisms. Another benefit of B. subtilis was that the cells didn’t have to be popped, this reduces the hardware component estimates that our (Isaac’s) crude idea began with.

We had brainstorming sessions with Manu Prakash which helped to narrow down our project into looking for the harder tasks. He suggested that quantifying and purifying the production of our enzymes would be a critical aspect, as well as building a frugal chromatographic column. We were very excited when we got to speak to Dushanth Seervaratnam, who had built a frugal chromatography column purifying based on Silica tags which can be readily, and frugally, made from Sand.

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!

Part II: When you build a team with people from all over the world every meeting become an Integrated Human Practice

As one can imagine, when you bring together people from 10 different countries, all with different backgrounds, every meeting and decision becomes very well discussed in its diverse aspects. This is how we managed to have so many different areas within SynBio covered by Friendzymes. It is because of the expertise of the group's Software Engineers and Bioinformaticians that we have been able to develop work in the Software section that goes through different levels of programming knowledge: The Friendzymes Cookbook, for beginner programmers, and Friendzymes Actions for large-scale circuit design analysis for those more advanced (see Software and Education for more details). This diversity also opens us to members who are interested in hardware development, which has allowed us to build two different types of bioreactors. Once these two bioreactors are developed and the problem areas fixed, we intend to analyze and compare their quality and feasibility (see Hardware ). Finally, it is because one of the leaders (and creator of the project) and also our PI Scott were previously associated with Free Genes and the Open Bioeconomy Lab that we already had a library available (see the B. subtilis Protein Secretion Toolkit ), which also provides shipping around the world.

As you can see, the more our team grew in numbers and consisted of a wider audience, the more our project began to develop a global perspective. During meetings and co-working, we noticed that a single question arose time and time again: “what does democratized biotechnology mean?” While this was a single question, there was no single answer. This was where we saw that “democratized biotechnology” could mean different things, since each person saw it in a different light, depending on where s/he was from.

Those from high-income countries viewed “Democratized Biotechnology” as a means to provide community labs or biohacking spaces with cheaper alternatives for their work since they often don't have funding from large institutions. This perspective is exciting as it can introduce many niches in biotechnology.

However, that was a completely different view from our members who were from resource-constrained areas (e.g. Brazil, Philippines) where the currency was weaker than the USD dollar - the most common currency for purchasing laboratory supplies. For them, democratizing Biotechnology meant giving even their biggest labs' possibility to have the very basic tools, as these places suffered not only with the currency but also with a general lack of financing; the difficulty of importation (including high shipping rates); and the difficulties of transporting biological materials, e.g. if the product has to be kept at low temperatures. Thus, in these places, the amount paid can be around double in comparison to what labs in the US/Europe pay for reagents; and the ability to manufacture some reagents locally through synthetic biology relieves this problem.

Friendzymes as a whole soon realized the importance of those exchanges as both views provided insight on what impact our project will have depending on the country; therefore, perspectives are taken into consideration when attempting to democratize biotechnology for all. Given the international, diverse, and heterogeneous nature of Friendzymes (see Diversity section ), we were able to see this vividly. We found ourselves with priceless resources, our team. Everyone had something they could teach, enthusiasm to learn, and diversity so beneficial as to help all learn more about the world we live in.

Part III: The journey continues - People who were essential for the further development of the iGEM Project

The Frugal Science class was over, but our team's journey continued. We have discussed the project with many people since then, only now in a more iGEM-driven manner, to develop the best possible project. From here, we have categorized individual collaborations by theme.


Dan Ziegler

Dan Ziegler has been studying bacillus for over 30 years and is the director of Bacillus Genetic Stock Center. We ​​had a conversation that was filled with many important pieces of information about the various species and ubiquity, diverse life-cycle paths signal cascades, biotechnological history of this organism (fun fact: it was discovered in the 1800s as it was growing out of oil hay infusions), problems regarding sporulation, proteases, competence, induction, and biofilms with B. subtilis and how to get around those for our project goals. Although the information regarding signal peptides strengthened and supported the original plan, our wetware design approach was flipped on its head after this talk as he advised conjugating our plasmid rather than transforming it from E. coli into bacillus, which led to more us pondering whether we should pursue genomic integration of our construct or not. We were also granted a handful of resources (check out Subtillery - an annual conference devoted to Bacillus Subtilis!) including a collection of shuttle vectors from E. coli to B. subtilis, references to many B. subtilis genetic toolboxes out there, and a detailed overview of lab protocol when working with the organism! Furthermore, he suggested a few potential future projects with Bacillus subtilis that could be helpful and impactful to the platform.

Anthony Di Franco (Open Insulin)

One of Friendzymes partners is the Open Insulin Project, a collection of researchers and advocates developing open-sourced protocols for producing insulin. With the high demand of insulin coupled with the high costs, we thought it prudent to partner with Open Insulin as the frugal production and distribution of insulin can help many around the world.

In our conversation with Anthony Di Franco, the creator of Open Insulin, we discovered that insulin must be produced in a facility with high quality and safety standards to be usable.

Since this would be very difficult to implement at this stage of our project, we elected to focus on other goals and leave this for a later date.

Despite this change in focus, this meeting was still valuable for Friendzymes and Open Insulin as we exchanged ideas on the many ways of managing a large group and keeping people engaged in our cause.


Chaz Childers, Matthew Monsees and Lissette Bouza from Opentrons

An important part of the smooth operation of biofoundries is the speed and reproducibility of the processes. This is why we were leaning towards the idea of automating the processes of our prototypes, and nothing can help this more than robots! We decided to talk to some representatives from Opentrons because their goals and values are very closely aligned with Friendzymes'.

We were further assured of our alignment in goals and the use of robots when talking to Chaz Childers (Manager of Applications Engineering Team) and Matthew Monsees (Director of Marketing). We had important dialogs, especially on software development, and started to theorize how design and experiments/protocols could be better integrated with automated systems using OT-2s. This gave us a much clearer perspective on how to make frugal biofoundries more autonomous. You can see in the Software section what we built based on this exchange.

Also, with this partnership, Opentrons donated 2 OT-2s to the labs in Ghana and Philippines, as well as pipettors and consumables for all the labs (besides the two mentioned, Chicago (US) and Vancouver (CA). Additionally, Lissette Bouza, an incredibly helpful Customer Success Manager of Opentrons, helped Friendzymes to develop specific protocols and python scripts required for our project needs.

More than a sponsorship, these materials will help ensure the implementation of our frugal biofoundries around the world, and for that we are very grateful to the whole Opentrons team!

Sebastian Cocioba from Binomica Labs

Sebastian Cocioba is a researcher and plant genetic engineer who we connected with questions about DIY bioreactors and he is happy to be a friend of Friendzymes!

In developing a bioreactor, Sebastian recommended using a flat 4L bottle, like a thin carboy, and two heating panels on either side to allow for a more even distribution of heat and adding some insulating product such as mylar. According to Sebastian, this provided a stable heating to 37.0℃ ± 0.2℃ in about 25 min. In order to show that his process worked, Sebastian used a fluorescent protein that required aeration for the reaction to proceed. He produced aeration in his bioreactor by using an air stone from his aquarium, sterilizing it, and then adding it to the bottle. Sebastian was able to successfully produce the desired reaction in his homemade bioreactor for about $100 USD, for a project focused on frugal biotechnology, such as Friendzymes, this was just what we were looking for! Sebastian’s purchases were from Amazon, however, if we purchased the same products from a source such as Alibaba, he estimates that the cost would be around $40 USD. Unfortunately, due to his client dropping the project, Sebastian wasn’t able to continue developing the bioreactor by improving the code for the arduino, temperature controls, developing a cleaner way to remove the finished product from the bottle, and more. However, he has sent us the code that he was using for his systems so we could work on what he developed and adjust it for our needs.

While Sebastian’s homemade bioreactor could be heated, it had no active cooling capabilities. In order for cooling to occur some other process will need to be implemented and possible solutions were discussed such as using controlled airflow to regulate temperature. However, active cooling requires a lot more parts and a lot more maintenance, which is disadvantageous for frugal labs in rural areas. When thinking about frugal biotechnology for all, understanding how each of these processes should be adapted for various climates and economies is crucial for its successful implementation.

According to Sebastian's recommendations, the work developed on the bioreactor described in our Hardware section uses a 4L container, an insulating product for the container, and an aquarium air stone to agitate and oxygenate the biological system. Overall, our whole Hardware section was (and will continue to be) highly inspired by Sebastian, since not only this specific work of his is useful, but also much of what he advocates and creates in an open and shared way is extremely important.


Timothy Styles

Timothy Stiles is the creator of the tool we are using as the basis for building our software pipelines and also the tool we have chosen to improve and contribute to - the (Poly)merase package. We have a good reason for this. Tim showed that there was a bottleneck among SynBio researchers due to the lack of a unified code language and software library specific to this scientific approach. Also, before Poly, there was no way to convert Genbank files into open standard JSON file format and data exchange format. There were several discussions with Timothy and part of these discussions ended up generating contributions of functions, tests, and fixes that were integrated into later versions of Poly's source code. One of these is the integration of harpin-checking functions for correcting coding regions, now present in Poly.

Vinoo Selvarajah

A very intriguing connection we wanted to make was with Vinoo Selvarajah , Director of the iGEM Registry. This is because the software team has been following the work of adapting the current registry parts repository to the new — and open! — format under Free Projects. We noticed that the new repository is being developed using GitHub Actions, which allows automating pipelines. Our talk with Vinoo was very influential, as this inspired us to further investigate the use of these automated pipelines for the parts design task, and subsequently deciding to translate part of our scripts to the GitHub Actions format.

Our work with GitHub actions is explained in the Software section our Software section. and available for use.


Thomas Landrain, Leo Blondel, Paige Perillat-Piratoine and Heloisa Oss-Boll from JOGL

As our name - Friendzymes - suggests, we like to make friends around the world, because building a strong and active community is an essential part of achieving our goal of democratizing Synthetic Biology.

We decided to open up the scope of the project beyond the usual platforms and use JOGL (Just One Giant Lab), an open community filled with people from all over the globe who want to do collaborative scientific work. We created a space for the project that can be accessed by anyone who is interested; additionaly, we opened a challenge - proposing that anyone interested in building low-cost plate-readers can create their own model and participate in our goal.

None of this would have been possible without the idea and encouragement of Thomas Landrain (Co-Founder and CEO) and Leo Blondel (Co-Founder and CTO) who drove the creation of the Friendzymes’ JOGL Space. Paige Perillat-Piratoine (Community and Outreach) was essential for tips on how to improve our space in the future to get more engagement with other people and Heloísa Oss-Boll (Intern Community and Outreach) was an important partner who proposed that we host an event to talk about frugal biofoundries with people around the world using the JOGL platform. This inspired us to do it in the format of a hackathon so that we could interact with and meet everyone! Heloísa and Paige helped Friendzymes as we embarked on the journey of making the hackathon happen by giving us several tips. Shrestha Rath (Intern Community and Outreach) is also one of the organizers of the Global Policy Mapping Hackathon at After iGEM also provided us with good insights, primarily related to good documentation and guides for hackathon participants, as well as picking a winner because it would encourage participants to develop good project concepts.

Finally, Chris LB Graham (Co-founder of Helpful Engineering and JOGL Community based Grant Review) was instrumental in how we decided on the winning project at the hackathon. Chris is the creator of a Community Peer Review system and guided us on how to do this with the projects developed at the hackathon.

Robert Lee Read

Robert is the Head Coach of Public Invention, a nonprofit that invents in the public, for the public. They make collaborative teams that make new inventions possible with free and open hardware. Rob is also from the board of directors of Helpful Engineering, a global non-profit community whose mission is to collectively engineer rapid and open solutions to sustainability challenges worldwide. Rob connected us wonderful people at Helpful Engineering to help our hardware side of the team to brainstorm prototypes further! He also gave Friendzymes good advice on how to conduct funding request meetings, provided input on frugal materials we could use for our bioreactors, and we got to learn about ways to fund our hardware prototypes as we were introduced to a community of hardware tinkerers with whom we will be continuing our hardware explorations beyond iGEM.

Part IV: looking into the future and beyond

We had the opportunity to meet with Alexis Casas, from the London Biofoundry. He talked about how he had been advising the iGEM 2021 Paris Bettencourt (and iGEM 2021 Marburg) teams on making a network of distributed biofoundries and remote labs, and the differences between implementations related to Friendzymes distributed laboratories and London Biofoundry. This actually culminated in a collaboration after the Computational Modeling in Biology Network (COMBINE) meeting to create executable and unified standard protocols (PAML) that could be easily integrated into different lab/biofoundry setups, including the 4 Friendzymes laboratories, the London Biofoundry, and Tim Dobbs from CRI Paris.

Also, after the hackathon that we organized with JOGL (see more detail in the Education section), we found ourselves leaning closer and closer to the conclusion that the mass manufacturing of enzymes, and the research on how to produce low-cost equipment for Biofoundries, could have a greater impact than previously imagined. The number of people that participated in the event let us realize that many people were interested in our proposition and that the Friendzymes’ objectives resonated with a global audience. A proposal raised by Devin Camenares suggested that one application of free enzyme production could be the introduction of biotechnological tools and methodologies in high schools, bringing new light to science apprenticeship.

The ideas proposed during the Hackathon have not had time to show their impact on the project; however, the proposed applications that were presented helped Friendzymes to understand that our low-cost Frugal Biofoundries goal could be useful to address many modern issues, more than we ever imagined. We’ve worked alongside the teams to see how they came up with ideas to make bioengineering more accessible, and we couldn’t be happier with the results.

Then, the enzymes and low-cost equipments we made during the project will serve as the foundation for friendzymes teammates’ future projects, and we’re sure that we’ll look into the future with the vision of using the tools and knowledge learned here to build a better world.