Difference between revisions of "Team:Cambridge-JIC/Integrated Practices"

 
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     <p style="font-family:Arvo ; font-size:160%; text-align:center">In order to integrate best practices for open hardware design within our protocols, we spoke to Tobias Wenzel, co-founder of <a href="http://docubricks.com/" class="darkBlue" style="font-size:100%;">DocuBricks</a>; a website for high quality open source documentation, funded by the OpenPlant program. See what we discussed in the interview:</p>
 
     <p style="font-family:Arvo ; font-size:160%; text-align:center">In order to integrate best practices for open hardware design within our protocols, we spoke to Tobias Wenzel, co-founder of <a href="http://docubricks.com/" class="darkBlue" style="font-size:100%;">DocuBricks</a>; a website for high quality open source documentation, funded by the OpenPlant program. See what we discussed in the interview:</p>
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         <h2 style="font-family:Pacifico ; text-align: center">How we integrated this into our design:</h2>
 
         <h2 style="font-family:Pacifico ; text-align: center">How we integrated this into our design:</h2>
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           <li>Bring together biologists, engineers, technologists and others in the Cambridge area for meeting, co-working and socialising in a creative, cross-disciplinary, community-driven and safe environment.
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           <li>Provide a well-equipped space for practical biology and engineering of biology on a community membership basis.
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          <p style="font-family:Arvo; font-size:130%; text-align:center">Neglect of safety features in open source protocols  - as well as the features already included in our designs from community lab feedback, such as contained electrical connections and safety shields, we included instructions on how users can conduct <span class="darkBlue">isolated safety checks</span> when building our hardware. For example, underwater pressure testing of the gun and checking of electrical circuits.</p>
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          <li>Support new and existing interdisciplinary collaborations for engineering biology, with a focus on promoting open technology and innovation.
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           <li>Raise awareness, understanding and participation in biology and engineering of biology in the Cambridge area through public engagement activities, education and training.
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          <p style="font-family:Arvo; font-size:130%; text-align:center">Encouragement of designers to document their hardware properly - in addition to our own protocols, we have included <span class="darkBlue">links on our wiki to DocuBricks</span> and an easy-to-follow <span class="darkBlue">checklist of components</span> for anyone considering writing their own open source protocol.</p>
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           <li>Foster links with local industry and innovation organisations, building bridges between academia and bioenterprise.
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          <p style="font-family:Arvo; font-size:130%; text-align:center">Adaptability of our design for different end users - including <span class="darkBlue">alternative supplier links</span> for parts, where possible, to suit international users of the hardware and also providing an alternative in case the primarily-suggested supplier is out of stock.</p>
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          <p style="font-family:Arvo; font-size:130%; text-align:center">Used open source software when designing CAD files for parts of the gene gun and growth facility, so these files can be downloaded and customised by anyone.</p>
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         <h2 style="font-family:Pacifico ; text-align: center">OpenPlant</h2>
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         <h2 style="font-family:Pacifico ; text-align: center">Designing for the DIY Bio Community</h2>
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         <h3 style="font-family:Pacifico ; text-align: center">Understanding the bottlenecks of plant synthetic biology and best practices for open science</h3>
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        <p>Hosted at the John Innes Centre in Norwich, the OpenPlant Forum presented talks from some of the most exciting innovations and research developing in plant synthetic biology at this moment. The three-day event also featured panel discussions on predominant issues in this field, including a discussion on “Commercial opportunities and bottlenecks in the future of plant synthetic biology”, featuring the inventor of BioBricks and ‘godfather’ of synthetic biology, Tom Knight.</p>
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          <p style="font-family:Arvo; font-size:130%; text-align:center">In order to best understand the requirements for our hardware, we contacted community labs from around the world to inform them about our project and find out the features they wanted to see in our designs.</p>
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        <img src="https://static.igem.org/mediawiki/2016/6/61/T--Cambridge-JIC--HP3_1.png" style="display:block; margin-left:auto; margin-right:auto; max-width:100%; max-height:100%">
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          <p style="font-family:Arvo; font-size:130%; text-align:center">We contacted the labs listed in the table below, asking about their current experience with plant synthetic biology, existing laboratory resources and technical experience in building hardware. This was to ensure we were creating accessible designs, both financially and in their technical demands for construction, that would definitely fulfill a real need for these groups.</p>
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          <p style="font-family:Arvo; font-size:130%; text-align:center">The full survey and information about our project sent to these labs can be seen <a target="_blank" href="https://static.igem.org/mediawiki/2016/9/99/T--Cambridge-JIC--HP--Questions.docx">here</a>.</p>
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        <p>This discussion raised the need for creating more efficient techniques for engineering plants into chassis for commercial production of biofuels and pharmaceuticals. This is something which we already aim to achieve as part of our project, through a standardised cas9 system for chloroplast engineering, which follows the phytobrick common syntax. Other relevant challenges were also raised in the discussion on “Reprogramming Agriculture”, such as responsible research and public perception of plant synthetic biology. Members of our team took part in this talk, sharing our views with an audience of over 100 people and making the key point that scientists have a responsibility to document their research and methods thoroughly. Mistrust and misunderstanding of what plant synthetic biology will be used for, and the ownership of this technology, is a result of miscommunication between the scientific and nonscientific communities.</p>
 
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        <p>The discussions highlighted the importance of  DIY Bio Hackspaces, such as those we had encountered at the Bio NightScience event in Paris.  By allowing ‘ordinary’ citizens to actively participate in synthetic biology projects for themselves, this helps to bridge the gap between the two communities and create a dialogue between them. This further encouraged our design of a low cost growth facility and gene gun for such spaces, as any techniques for plant engineering which industry hopes to commercialise must first be widely accepted in the public eye. Providing accessibility to these techniques for hackspaces, schools and other small community labs will, we hope, promote more widespread understanding and acceptance of them.</p>
 
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        <p>Furthermore, hearing Tobias Wenzel, founder of Docubricks, speak at the OpenPlant Forum gave us the idea to use this format as a template for the documentation of our open source designs. We hope that integrating the same best practices for open documentation used by this site into our own project will help to further support our efforts in removing the bottlenecks to chloroplast engineering, by changing public reaction and accessibility to the technology.</p>
 
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         <h2 style="font-family:Pacifico ; text-align: center">Synthetic Biology Society</h2>
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          <TH><b>Organisation</b></TH>
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         <p>Synthetic biology society is a group of students at the University of Cambridge aiming to bring together biologists, engineers, physicists, computer scientists and others to work in synthetic biology and share knowledge. It has been established by previous iGEM members in 2015. The society has ambitions to raise awareness about synthetic biology amongst students, broaden their knowledge through talks and as probably the only Cambridge science society it is actively working on primary research projects.</p>  
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          <TH><b>Contact</b></TH>
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        <p>A few of our members got involved over the year with society’s activities and helped a bit with its beginnings and Lucie is on the current committee as the project manager. Last year’s project still in progress involves building a computer-navigated microscope moving in all three dimensions and scanning samples. Apart from continuing this we are planning a wetlab project in Biomakespace (have a link) which wants to explore cell-free systems. The project may change slightly but we want to make and tune a simple light oscillator (probably using fluorescent proteins fused to luciferase for sharper output changes) and also build a physical electric circuit imitating the biological system. From there we can study and demonstrate if the two systems behave and can be regulated similarly or differently, which may have a big educational value, we could also concentrate on transferring the system into a living organism or even some design using multiple oscillators. The emphasis in the project will be put on sharing skills, learning (even through seminars and trainings) and exploring what synthetic biology and scientific work in a team are all about!</p>
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          <TH><b>Feedback/Comments</b></TH>
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          <TH><b>Comments integrated into project design</b></TH>
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          <TD>The Lab, LA's Hub for Citizen Science and DIYBio</TD>
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          <TD>Cory Tobin</TD>
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          <TD>Wide range of technical skills in their hackspace and interest in DIY bio hardware, but strong budget constraints on building devices. <br><br>Full survey response <a target="_blank" href="https://static.igem.org/mediawiki/2016/a/ae/T--Cambridge-JIC--HP--response1.docx">download</a></TD>
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          <TD>Ensuring low cost of designs and thorough documentation of all the parts used</TD>
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          <TD>London BioHackspace<</TD>
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          <TD>Tom Hodder</TD>
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          <TD>Previous experience of building open source designs, such as openPump syringe, and strong interest in building our designs. <br><br>Full survey response <a target="_blank" href="https://static.igem.org/mediawiki/2016/a/ae/T--Cambridge-JIC--HP--response2.docx">download</a></TD>
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          <TD>Ensuring low cost of designs (below 500 GDP specifically for the gene gun), and consumables required for these</TD>
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          <TD>bioCURIOUS, Silicon Valley</TD>
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          <TD>Jay Hanson</TD>
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          <TD>Previously built their own DIY gene gun and have published this at their <a target="_blank" href="https://www.oreilly.com/ideas/how-to-build-and-use-a-gene-gun">website</a></TD>
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          <TD>Need for achieving pressure >100 psi in order to penetrate plant cells (from their own testing experience)</TD>
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          <TD>Bioflux Society, Berlin</TD>
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          <TD>Alessandro Volpato</TD>
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          <TD>Interest in receiving our design and lab protocols, and in working with microalgae</TD>
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          <TD>Integrating more safety features into the design, and checking these with thorough pressure testing</TD>
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Latest revision as of 21:36, 15 October 2016

Cambridge-JIC

INTEGRATED PRACTICES

Docubricks: Opening up the technology

In order to integrate best practices for open hardware design within our protocols, we spoke to Tobias Wenzel, co-founder of DocuBricks; a website for high quality open source documentation, funded by the OpenPlant program. See what we discussed in the interview:

How we integrated this into our design:

Neglect of safety features in open source protocols - as well as the features already included in our designs from community lab feedback, such as contained electrical connections and safety shields, we included instructions on how users can conduct isolated safety checks when building our hardware. For example, underwater pressure testing of the gun and checking of electrical circuits.

Encouragement of designers to document their hardware properly - in addition to our own protocols, we have included links on our wiki to DocuBricks and an easy-to-follow checklist of components for anyone considering writing their own open source protocol.

Adaptability of our design for different end users - including alternative supplier links for parts, where possible, to suit international users of the hardware and also providing an alternative in case the primarily-suggested supplier is out of stock.

Used open source software when designing CAD files for parts of the gene gun and growth facility, so these files can be downloaded and customised by anyone.



Designing for the DIY Bio Community

In order to best understand the requirements for our hardware, we contacted community labs from around the world to inform them about our project and find out the features they wanted to see in our designs.

We contacted the labs listed in the table below, asking about their current experience with plant synthetic biology, existing laboratory resources and technical experience in building hardware. This was to ensure we were creating accessible designs, both financially and in their technical demands for construction, that would definitely fulfill a real need for these groups.

The full survey and information about our project sent to these labs can be seen here.


Organisation Contact Feedback/Comments Comments integrated into project design
The Lab, LA's Hub for Citizen Science and DIYBio Cory Tobin Wide range of technical skills in their hackspace and interest in DIY bio hardware, but strong budget constraints on building devices.

Full survey response download		 Ensuring low cost of designs and thorough documentation of all the parts used
London BioHackspace< Tom Hodder Previous experience of building open source designs, such as openPump syringe, and strong interest in building our designs.

Full survey response download		 Ensuring low cost of designs (below 500 GDP specifically for the gene gun), and consumables required for these
bioCURIOUS, Silicon Valley Jay Hanson Previously built their own DIY gene gun and have published this at their website Need for achieving pressure >100 psi in order to penetrate plant cells (from their own testing experience)
Bioflux Society, Berlin Alessandro Volpato Interest in receiving our design and lab protocols, and in working with microalgae Integrating more safety features into the design, and checking these with thorough pressure testing