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| 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.</p> | | 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.</p> |
| <p> | | <p> |
− | Our plan was to provide anyone interested in harnessing biotechnology with more knowledge in how to <a href=”https://2021.igem.org/Team:Open_Science_Global/Engineering”>engineer biology</a>, the <a href=”https://2021.igem.org/Team:Open_Science_Global/Software”>software</a> to help in designing genetic constructs, and the means to produce the necessary equipment/<a href=”https://2021.igem.org/Team:Open_Science_Global/Hardware”>hardware</a> to set up their own frugal bio-toolkit or bio-foundry. | + | Our plan was to provide anyone interested in harnessing biotechnology with more knowledge in how to <a href="https://2021.igem.org/Team:Open_Science_Global/Engineering">engineer biology</a>, the <a href="https://2021.igem.org/Team:Open_Science_Global/Software">software</a> to help in designing genetic constructs, and the means to produce the necessary equipment/<a href="https://2021.igem.org/Team:Open_Science_Global/Hardware">hardware</a> to set up their own frugal bio-toolkit or bio-foundry. |
| </p> | | </p> |
| | | |
| <p> | | <p> |
− | 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 <a href=”https://2021.igem.org/Team:Open_Science_Global/Human_Practices”>Frugal Biofoundries Hackathon</a>. | + | 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 <a href="https://2021.igem.org/Team:Open_Science_Global/Human_Practices">Frugal Biofoundries Hackathon</a>. |
| </p> | | </p> |
| <p> | | <p> |
− | 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 <a href=”https://2021.igem.org/Team:Open_Science_Global/Notebook”>how they would be able to do so</a>. | + | 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 <a href="https://2021.igem.org/Team:Open_Science_Global/Notebook">how they would be able to do so</a>. |
| 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. | | 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. |
| </p> | | </p> |
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| <br> | | <br> |
| <p><b>A. How can our software help the future iGEM teams?</b></p> | | <p><b>A. How can our software help the future iGEM teams?</b></p> |
− | <p>We have made <a href=”[link]”>“The Friendzymes Cookbook”</a> 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. </p> | + | <p>We have made <a href="https://github.com/Open-Science-Global">"The Friendzymes Cookbook"</a> 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. </p> |
− | <p>The following 6 separate <a href=”[link]”>colab/jupyter notebooks</a> 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.</p> | + | <p>The following 6 separate <a href="https://github.com/Open-Science-Global">colab/jupyter notebooks</a> 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.</p> |
| <br> | | <br> |
| <p><b>B. How can our hardware help future iGEM teams?</b></p> | | <p><b>B. How can our hardware help future iGEM teams?</b></p> |
− | <p>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 <a href=”https://2021.igem.org/Team:Open_Science_Global/Hardware”>Hardware</a> 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. </p> | + | <p>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 <a href="https://2021.igem.org/Team:Open_Science_Global/Hardware">Hardware</a> 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. </p> |
| <br> | | <br> |
| <p><b>C. How can other iGEM teams use the wetware/polymerase we created?</b><p> | | <p><b>C. How can other iGEM teams use the wetware/polymerase we created?</b><p> |
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| <p><b>D. How can you set up, organise and implement your internationally distributed project?</b></p> | | <p><b>D. How can you set up, organise and implement your internationally distributed project?</b></p> |
− | <p>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 <a href=”https://2021.igem.org/Team:Open_Science_Global/Inclusivity”>Diversity</a> page where the future iGEM teams can take note and expand their project to a global scale. </p> | + | <p>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 <a href="https://2021.igem.org/Team:Open_Science_Global/Inclusivity">Diversity</a> page where the future iGEM teams can take note and expand their project to a global scale. </p> |
− | <p>We also recently started discussions with Alexis Casas, who has been advising the <a href=”https://2021.igem.org/Team:Paris_Bettencourt”>iGEM 2021 Paris Bettencourt</a> (and <a href=”https://2021.igem.org/Team:Marburg”>iGEM 2021 Marburg</a>) 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. </p> | + | <p>We also recently started discussions with Alexis Casas, who has been advising the <a href="https://2021.igem.org/Team:Paris_Bettencourt">iGEM 2021 Paris Bettencourt</a> (and <a href="https://2021.igem.org/Team:Marburg">iGEM 2021 Marburg</a>) 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. </p> |
| <br> | | <br> |
| <p><b>E. How can you use our entrepreneurship efforts to start your company? </b></p> | | <p><b>E. How can you use our entrepreneurship efforts to start your company? </b></p> |
− | <p>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. </p> | + | <p>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. </p> |
| </div> | | </div> |
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| <p><b>A. How can the world benefit from our software?</b></p> | | <p><b>A. How can the world benefit from our software?</b></p> |
| <p>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. </p> | | <p>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. </p> |
− | <p>This was made possible only because our software is open-source and is built on <a href=”https://github.com/TimothyStiles/poly”>Poly</a>. 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. </p> | + | <p>This was made possible only because our software is open-source and is built on <a href="https://github.com/TimothyStiles/poly">Poly</a>. 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. </p> |
| <br> | | <br> |
| <p><b>B. How can the world benefit from our Human practices outreach?</b></p> | | <p><b>B. How can the world benefit from our Human practices outreach?</b></p> |
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| <p><b>C. How can our wetware parts collection help the real world?</b></p> | | <p><b>C. How can our wetware parts collection help the real world?</b></p> |
| <p>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. </p> | | <p>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. </p> |
− | <p>To this end, we have developed a library of sec tags - Bacillus Toolkit, based on work by <a href=”https://pubmed.ncbi.nlm.nih.gov/16930615/”> Brockmeier et al. 2006</a>. The sec tags were codon optimised using the <a href=”https://2021.igem.org/Team:Open_Science_Global/Software”>software</a> we developed, and we have added our contributions to the <a href=”https://stanford.freegenes.org/collections/all/products/b-subtilis-protein-secretion-toolkit#description”>FreeGenes</a> website, such that our library of sec tag genetic constructs can be easily, and freely, shipped to researchers around the world. </p> | + | <p>To this end, we have developed a library of sec tags - Bacillus Toolkit, based on work by <a href="https://pubmed.ncbi.nlm.nih.gov/16930615/"> Brockmeier et al. 2006</a>. The sec tags were codon optimised using the <a href="https://2021.igem.org/Team:Open_Science_Global/Software">software</a> we developed, and we have added our contributions to the <a href="https://stanford.freegenes.org/collections/all/products/b-subtilis-protein-secretion-toolkit#description">FreeGenes</a> website, such that our library of sec tag genetic constructs can be easily, and freely, shipped to researchers around the world. </p> |
| <br> | | <br> |
| <p>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: <a href="https://discord.gg/unBRDYdrhX">https://discord.gg/unBRDYdrhX</a>. </p> | | <p>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: <a href="https://discord.gg/unBRDYdrhX">https://discord.gg/unBRDYdrhX</a>. </p> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Attributions”>Attributions</a></b> </td> <td> Our Friendzymes team have had support from many people throughout our project, from X to Y to Z. We would like to express our gratitude to all these people for the advice, discussions, and support on our <a href=”https://2021.igem.org/Team:Open_Science_Global/Attributions”>Attributions</a> page. </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Attributions">Attributions</a></b> </td> <td> Our Friendzymes team have had support from many people throughout our project, from X to Y to Z. We would like to express our gratitude to all these people for the advice, discussions, and support on our <a href="https://2021.igem.org/Team:Open_Science_Global/Attributions">Attributions</a> page. </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Description”>Description </a></b></td> <td> Our <a href=”https://2021.igem.org/Team:Open_Science_Global/Description”>project description</a> provides a general overview of the goals that our Friendzymes team set out to achieve. …</td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Description">Description </a></b></td> <td> Our <a href="https://2021.igem.org/Team:Open_Science_Global/Description">project description</a> provides a general overview of the goals that our Friendzymes team set out to achieve. …</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Contribution”>Contribution </a></b></td> <td>From our <a href=”https://2021.igem.org/Team:Open_Science_Global/Contribution”>Contributions</a> page, we hope you can 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. … </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Contribution">Contribution </a></b></td> <td>From our <a href="https://2021.igem.org/Team:Open_Science_Global/Contribution">Contributions</a> page, we hope you can 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. … </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Engineering”>Engineering </a></b></td> <td>From our <a href=”https://2021.igem.org/Team:Open_Science_Global/Engineering”>Engineering </a> page, you can find out more of how we planned to develop our experimental work, following the DBTL cycle… </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Engineering">Engineering </a></b></td> <td>From our <a href="https://2021.igem.org/Team:Open_Science_Global/Engineering">Engineering </a> page, you can find out more of how we planned to develop our experimental work, following the DBTL cycle… </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Collaborations”>Collaborations</a> </b></td> <td> More details… </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Collaborations">Collaborations</a> </b></td> <td> More details… </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Human_Practices”>Human Practices </a></b></td> <td> More details… </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Human_Practices">Human Practices </a></b></td> <td> More details… </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Implementation”>Implementation</a> </b></td> <td>More details… </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Implementation">Implementation</a> </b></td> <td>More details… </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Human_Practices”>Integrated Human Practices</a> </b></td> <td>More details… </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Human_Practices">Integrated Human Practices</a> </b></td> <td>More details… </td> |
| </tr> | | </tr> |
| | | |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Proof_Of_Concept”>Proof of Concept</a> </b></td> <td>More details… </td> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Proof_Of_Concept">Proof of Concept</a> </b></td> <td>More details… </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td> <b><a href=”https://2021.igem.org/Team:Open_Science_Global/Communication”>Education and Communication</a></b> </td> <td> <b>Education</b><br> | + | <td> <b><a href="https://2021.igem.org/Team:Open_Science_Global/Communication">Education and Communication</a></b> </td> <td> <b>Education</b><br> |
| Education resources that we have contributed too include: | | Education resources that we have contributed too include: |
| <ul> | | <ul> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
− | <td><b><a href=”https://2021.igem.org/Team:Open_Science_Global/Excellence”> Excellence in another area </a></b></td> <td> Our excellence focus was on Diversity and Inclusivity… </td> | + | <td><b><a href="https://2021.igem.org/Team:Open_Science_Global/Excellence"> Excellence in another area </a></b></td> <td> Our excellence focus was on Diversity and Inclusivity… </td> |
| </tr> | | </tr> |
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