Summary
The core motivation behind our project is to enable people more easy access(/reduce the entry barrier/requirements) to learn how to develop their own biotechnological solutions to tackle local and global challenges around them.
Our plan was to provide anyone interested in harnessing biotechnology with more knowledge in how to engineer biology, the software to help in designing genetic constructs, and the means to produce the necessary equipment/hardware to set up their own frugal bio-toolkit or bio-foundry.
To gain a better understanding of the community views on bio-foundries and to educate the public about how individuals can set up their own local bio-foundry, we collaborated with JOGL to run a Frugal Biofoundries Hackathon.
We have open-sourced every part of our project, and have provided a case-study/proof-of-concept example (a DNA polymerase) to show anyone who wants to synthesize and extract their own proteins-of-interest how they would be able to do so.
Every aspect of our project was designed to try benefit society and future iGEM teams and to forge a better-shared future. Here, we give you a broad idea of our specific contribution for future iGEM teams, the world, and how you can contribute to our global effort to democratize biotechnology beyond iGEM.
Table of Contributions
| Criterion | Our Approach |
Attributions
(Bronze #2) | Our Friendzymes team have had support from many people throughout our project, from Opentrons to JOGL to the iGEM Foundation. We would like to express our gratitude to all these people for the advice, discussions, and support on our Attributions page. |
Description
(Bronze #3) | Our project description provides a general overview of the goals that our Friendzymes team set out to achieve. … |
Contribution
(Bronze #4) | From our Contributions page, you’ll be able to see how our software, wetware, hardware, and human practices approach has helped not only to develop our project ideas, but hopefully will be useful to other synthetic biology users for future iGEM teams and the wider community. |
Engineering
(Silver #1) | From our Engineering page you can find out more of how we planned to develop our experimental work, following the DBTL cycle, steps in the production, and much more! |
Collaborations
(Silver #2) | As a team that wanted to reflect the plurality of many different perspectives, one of our main goals was to connect with people, and we did so in our Collaborations page. There you’ll find every piece in the construction that is friendzmes, and how they contributed to us.
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Human Practices
(Silver #3) | One’s goal doesn’t rely on democratization without taking the societal/environment/political factors in consideration. Therefore our Human Practices page is where you can find all of our actions revolving around making the community grow, whether it is with education, whether it is with new propositions.
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Implementation
(Silver #4) | In this page you can see how we picture that our proposition would work if put in practice. How we define our protocols, the requirements and the perspectives and Implementations. |
Integrated Human Practices
(Gold #1) | Here in this session, you can find out more on how we expanded our plan of action to have the greatest positive impact in the SynBio community in our integrated human practices page.
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Proof of Concept
(Gold #4) | The proof of Concept page Is where all the information we gathered to support our claims to the applied approaches lie. There you can see lots of the work we did and the results of it. |
Education and Communication
(Gold #6) | Education
In the Education part you’ll find all about our projects with community engagement and how we tried our best to show people the marvels of frugal Bio Stacks and their applications.
You can also find out about the Hackathon we organized
Other teams and institutions involved
And the proposed Biofoundries applications according to the eyes of different teams around the world
Communication
In the Communications part you can take a look at Activities that we ran and held for the general public and the synthetic biology community:
All the talks we held and hosted in different platforms and in different events
All the documentation of our activities and their release free of charge for the general public to watch.
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Excellence in another area
(Gold #7) | Our excellence focus was on Diversity and Inclusivity. Our team knows no geographic borders so we focused on extracting the best out of each person's reality and seeing things from a different perspective, a global one. |
| iGEM Special Prizes | We thought long and hard about what our strengths were throughout our project, and we think that our team has a good chance at entering ourselves for these Special Prizes: Inclusivity, Integrated Human Practices, Software, Hardware, Education, and Entrepreneurship.
Please have a look and let us know what you think! |
For iGEM Teams
Our main contributions have been on all aspects of our project - software, hardware and genetic constructs. We nominate our software and hardware for the bronze requirements.
A. How can our software help the future iGEM teams?
We have made "The Friendzymes Cookbook" which is an educational tool for people to learn and perform Codon optimization, annotate problematic sequences, simulate Golden Gate reactions and ultimately make plasmids of their own from anywhere.
The following 6 separate colab/jupyter notebooks details how to run the open-source software tools we have developed. This can help future iGEM teams in their own genetic design process, which is a necessary component for every iGEM team.
B. How can our hardware help future iGEM teams?
We brainstormed with a lot of biotech enthusiasts and tinkerers through our human practices efforts and converged upon the hardware needed for a pipeline of enzyme synthesis and purification that we’ve documented in the Hardware section. This can be really useful for those iGEM teams that may be constrained by money and resources to develop the necessary basic enzymes in-house! We’ve documented the build of A frugal bioreactor, A plate reader and A Frugal chromatographic column, all of which can be manufactured within 2 to 3 weeks and under $4,000. These hardware components can also be built separately for other specific uses.
C. How can other iGEM teams use the wetware/polymerase we created?
Pfu_sso7d DNA Polymerase is off-patent, can be used commercially now. This is necessary. DNAP is necessary for PCR reactions, to amplify other genes of interest. It forms one of the enzymes needed in a bio-toolkit, along with ligases and restriction enzymes (some of which can now also be produced off-patent). We have submitted our DNAP construct to FreeGenes/Open Enzyme collection where future iGEM teams can obtain them for their uses. Even researchers around the world will benefit from them.
D. How can you set up, organise and implement your internationally distributed project?
We’ve had a rollercoaster of experience in making an internationally distributed team viable. While there were hurdles due to the whole project being done virtually and distributedly, we managed to turn them into our strength through the valuable lessons we learnt in this iGEM season. We’ve managed to document it in our Diversity page where the future iGEM teams can take note and expand their project to a global scale.
We also recently started discussions with Alexis Casas, who has been advising the iGEM 2021 Paris Bettencourt (and iGEM 2021 Marburg) teams on making a network of distributed biofoundries and remote labs. Had we heard about their work sooner, we would have engaged them to develop our individual projects into a partnership. Despite this, we intend to collaborate with them after iGEM 2021 to continue the work we started here.
E. How can you use our entrepreneurship efforts to start your company?
We have proposed the "Open Garage Door" model in our entrepreneurship efforts. Since, setting up bio-foundries in different parts of the world would require people to face different kinds of challenges, we have a "playbook" under construction where we will document information we gather and business models sustainable based on our discoveries. So far we have planned to use the "DIY Lean LaunchPad" idea of evidence-based entrepreneurship and have contributed by documenting it. Other teams can use the ideology behind DIY Lean LaunchPad towards handling a technical and a market-based solution.
For the world
Our project has always focused on the needs beyond iGEM. So, as a part of our iGEM journey, we made sure to contribute to the real world as we brought our project to life. While the above-mentioned contributions to future iGEM teams hold true for the broader synbio community as well, we’ve managed to go one step beyond to cater to real-world needs. Although the organisms used in our experiments are not pathogenic, the work environment and the chemicals used still pose risks to our researchers. Some examples of the chemicals used are hydrochloric acid (acidic) and sodium hydroxide (basic) to adjust the pH of buffers and growth media, some antibiotics, ethidium bromide and other chemicals commonly used in synthetic biology experiments. Our team received the proper training to handle these chemicals in a safer manner using the right equipment like smoke hoods, lab coats and gloves.
A. How can the world benefit from our software?
While the Colab notebooks we’ve created can be a great start to making your own optimised plasmid designs, it is not practical to be doing it in a Colab notebook for the real-world needs of thousands of genetic construct designs. We created a software component that is scalable - “Friendzymes Actions”. It is currently a set of 3 GitHub actions that can perform codon optimization. We have laid the foundation for more actions to be included in this pipeline to automate a lot more of plasmid designing by synbio enthusiasts around the world.
This was made possible only because our software is open-source and is built on Poly. Poly is a Go package for engineering organisms and has a community of developers and users who can help to get anyone started with contributing to it.
B. How can the world benefit from our Human practices outreach?
Our Human practices effort was an integral part for us to know the needs that different local communities have in setting up a bio-foundry. We believe that a frugal bio-foundry can help to efficiently automate the DBTL cycle which will be the go-to option for people outside traditional academic setups. So, we’ve managed to identify the problems that people would face in setting up a bio-foundry across the world and there are some Hackathon teams with great propositions of tackling such problems. Their solutions will help anyone to manifest a frugal bio-foundry to reality.
Our project idea has existed before iGEM and will continue beyond. So, we will be able to support those who want to set up frugal bio-foundries to create a more elaborate network of distributed bio-foundries part of our “bionet”.
C. How can our wetware parts collection help the real world?
One aspect of our work was to enable our proteins-of-interest to be expressed and secreted using Bacillus subtilis. When proteins are coupled with a secretion tag (sec tag), B. subtilis is able to extrude the proteins expressed in order for the proteins to be collected for use. However, different proteins may require different sec tags in order to be secreted efficiently.
To this end, we have developed a library of sec tags - Bacillus Toolkit, based on work by Brockmeier et al. 2006. The sec tags were codon optimised using the software we developed, and we have added our contributions to the FreeGenes website, such that our library of sec tag genetic constructs can be easily, and freely, shipped to researchers around the world.
On a concluding note, we aim to create a broader community of enthusiasts who want to democratize biotechnology along with us. To tackle frugalising enzyme production has just been the start of our journey. We operate mainly through Discord channel and anyone is free to join irrespective of their background knowledge. We want passionate people who want to envision a better future with us. This is the link to our discord channel: https://discord.gg/unBRDYdrhX.
