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| {{Marburg}} | | {{Marburg}} |
| <html> | | <html> |
− | <style>
| + | <div> |
− | hr { | + | <div class="box-dark"> |
− | display: block;
| + | <!--titel der seite--> |
− | height: 1px;
| + | <h1 class="heading"> |
− | border: 0;
| + | C L O N I N G<span style="visibility: hidden;">a</span>P R O T O C O L S |
− | border-top: 2px solid #3d404d;
| + | </h1> |
− | padding: 0;
| + | <hr class="line"> |
− | margin: 1em auto;
| + | <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Marburg--logo.svg" |
− | width: 50vw;
| + | class="logo" |
− | }
| + | alt="Syntex Logo"> |
− | | + | </div> |
− | @media (max-width: 810px) {
| + | <div style="margin-top: 11vh;"> |
− | }
| + | <center> |
− | </style>
| + | <h1 class="title">Cloning Protocols</h1> |
− | <div> | + | </center> |
− | <div class="box-dark">
| + | <section class="section"> |
− | <!--titel der seite-->
| + | <article> |
− | <h1 class="heading">
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
− | C L O N I N G<span style="visibility: hidden;">a</span>P R O T O C O L S
| + | Imagine its another iGEM day but instead of doing nightshifts you just press a button and your dozens of |
− | </h1>
| + | transformations are processed automatically. Imagine its another iGEM day but instead of plating out |
− | <hr class="line">
| + | mountains |
− | <img src="https://static.igem.org/mediawiki/2019/a/ac/T--Marburg--logo.svg" class="logo" alt="Syntex Logo">
| + | of plates you just press a button and plating is done by its own. Imagine its another iGEM day but instead |
| + | of |
| + | coming to work early you receive a notification on your phone that all your colonies were already picked and |
| + | your overnight cultures are currently going through a plasmid purification. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | Sounds like another weird dream from a crazy iGEM team, doesn’t it?<br> |
| + | Imagine how much time for designing and testing new constructs you would have !<br> |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | We want to contribute to this dream for the sake of the iGEM community. That's why we started this huge task |
| + | with the goal to fully automate the processes of building genetic constructs for this year’s iGEM project. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | We asked ourselves, which protocols need to be automated the most direly? |
| + | We started with small things, writing protocols for pipetting, PCR reactions, eventually combining parts in |
| + | a |
| + | one-pot Golden Gate reaction. To make it as user friendly as possible we wrote protocols that can be |
| + | adjusted by |
| + | a |
| + | graphical user interface (GUI). We upscaled these protocols to a level at which a single human person |
| + | would never be able to keep up the pace without making mistakes. Just think about setting up 96 golden |
| + | reactions |
| + | with 8 parts each, including buffer and enzymes. This would result in 1056 single pipetting steps for a |
| + | single |
| + | 96 well plate! |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | Continuing down this path we proceeded by automating the transformation protocol using chemically competent |
| + | cells and the Opentrons’ temperature module. An issue we encountered was the fast transition of the cells |
| + | from |
| + | low temperature to 42°C. We implemented the feedback of Keoni Gandall from Drew Endy’s lab in Stanford to |
| + | pipet the cells rapidly from the cooling block to the temperatur module. This should yield in the highest |
| + | transformation efficiency possible. We can now transform <i>E. coli</i> in a 96 well format at the same |
| + | time. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | The next milestone on our way was to go from a full 96 well plate to colonies on an agar plate. We had to |
| + | become |
| + | a little bit more creative with that: plating every transformation on a single plate was not a valid option |
| + | as |
| + | it would limit our scale pretty quickly. Additionally it is up to date impossible to streak out liquids on |
| + | an |
| + | agar plate with the Opentrons, which is the manual way that transformations are spread. We decided to follow |
| + | the |
| + | advice of Keoni to do 4 dilutions for every transformation and plate all of them on 4 SBS one-well agar |
| + | plates |
| + | by spotting 1 µl in an 12x8 array. The higher the dilutions, the fewer cells are spotted per drop, |
| + | eventually |
| + | resulting in single colonies. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | After having single colonies on our SBS plates, we also implemented <a style="padding: 0" |
| + | href="https://2019.igem.org/Team:Marburg/Colony_Picking">colony picking</a> and <a style="padding: 0" |
| + | href="https://2019.igem.org/Team:Marburg/Miniprep">plasmid purification</a> to finish the whole construct |
| + | building workflow. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | All these protocols for PCR reaction, Golden Gate assembly, transformation and plating are available with |
| + | detailed documentation on <a style="padding: 0" |
| + | href="https://github.com/igemsoftware2019/iGemMarburg2019">Github</a>, ready to |
| + | be implemented by other iGEMs team that share our dream of the “lights-out-laboratory”. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | We know that we are not saving the world with automating single steps in cloning processes, but we think |
| + | that these are some essential steps towards a future in which every iGEM team with an Opentrons robot can go |
| + | to the next level of automation thanks to all our <a |
| + | href="https://github.com/igemsoftware2019/iGemMarburg2019/tree/master/Hardware">hardware</a> and <a |
| + | href="https://github.com/igemsoftware2019/iGemMarburg2019/tree/master/AI">software</a> solutions. Our |
| + | vision is to free up their time to focus on designing even more awesome projects, achieving even greater |
| + | results, dreaming even bigger dreams. |
| + | </p> |
| + | </article> |
| + | </section> |
| + | </div> |
| + | <div style="margin-top: 10vh;"> |
| + | <center> |
| + | <h1 class="title">G.U.I.D.E - Graphical User Interface for Directed Engineering</h1> |
| + | </center> |
| + | <section class="section"> |
| + | <article> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | A large part of the work that we as biologists do in the laboratory consists of repetitive, monotonous, |
| + | mundane tasks. Imagine a world in which the scientist is liberated from these experiences and is able to |
| + | fully |
| + | concentrate on the important things of their project. Enter the world of automation. We firmly believe that |
| + | affordable lab automation will fundamentally change the field of biology as we know it today. In order for |
| + | this change to be a positive one, we consider it indispensable to take greater account of the end-user. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | Unfortunately, most of us had the experience that a great deal of software solutions in science are too |
| + | difficult to use and therefore discourage many potential users from the get go. |
| + | In order to tackle this problem, this year’s team has given a lot of thought into what makes a good user |
| + | experience and how to use this to bring our automation efforts to a wider audience. |
| + | Our project required a variety of Opentrons OT-2 protocols that range from simple dilution series to much |
| + | more |
| + | complex Golden Gate assemblies. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | To reconcile this diverse set of protocols without overwhelming the user, it requires intuitive software |
| + | that |
| + | packages modern features, such as drag and drop support, an easy to use deck overview and intelligently |
| + | groups |
| + | features that are more advanced. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | Fortunately, these ideas thoughts came around the same time as the invitation to the BioHackathon from <a |
| + | href="https://2019.igem.org/Team:Vilnius-Lithuania/Public_Engagement">iGEM Vilnius</a>, allowing us to put |
| + | them directly into practice. |
| + | The Hackathon gave us the unique opportunity to discuss our efforts with other iGEM teams and experts from |
| + | different disciplines, making it possible to immediately implement the feedback. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | We worked on an app were protocols can be integrated simply via drag and drop. |
| + | After successfully loading the protocol into its library, the user can see not only the labware used, but |
| + | also |
| + | the liquids and their correct position on the OT-2 deck. Additionally the applications allows for protocol |
| + | simulation, advanced code view and the change of variables |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | After just 3 days our prototype had many of the aforementioned features making the participation a |
| + | resounding |
| + | success. Later development allowed us to expand its functionality and smooth out its edges. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | The user interface (UI) is written in C# and can interface modified Opentrons protocols that are written in |
| + | python via json files that define variables such as labware and liquids. |
| + | In order to make the UI more visually appealing we designed multiple vector graphics of the labware and |
| + | robot. |
| + | </p> |
| + | <p style="text-align: justify; margin-bottom: 1em;"> |
| + | We believe that this is a step in the right direction for a more user-friendly automation environment and |
| + | hope |
| + | to build upon this experience to expand this project in the upcoming years. |
| + | </p> |
| + | </article> |
| + | </section> |
| + | </div> |
| </div> | | </div> |
− | <div style="margin-top: 11vh;">
| |
− | <center>
| |
− | <h1 class="title">Cloning Protocols</h1>
| |
− | </center>
| |
− | <section class="section">
| |
− | <article>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | Imagine its another iGEM day but instead of doing nightshifts you just press a button and your dozens of
| |
− | transformations are processed automatically. Imagine its another iGEM day but instead of plating out mountains
| |
− | of plates you just press a button and plating is done by its own. Imagine its another iGEM day but instead of
| |
− | coming to work early you receive a notification on your phone that all your colonies were already picked and
| |
− | your overnight cultures are currently going through a plasmid purification.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | Sounds like another weird dream from a crazy iGEM team, doesn’t it?<br>
| |
− | Imagine how much time for designing and testing new constructs you would have !<br>
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | We want to contribute to this dream for the sake of the iGEM community. That's why we started this huge task
| |
− | with the goal to fully automate the processes of building genetic constructs for this year’s iGEM project.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | We asked ourselves, which protocols need to be automated the most direly?
| |
− | We started with small things, writing protocols for pipetting, PCR reactions, eventually combining parts in a
| |
− | one-pot Golden Gate reaction. To make it as user friendly as possible we wrote protocols that can be adjusted by
| |
− | a
| |
− | graphical user interface (GUI). We upscaled these protocols to a level at which a single human person
| |
− | would never be able to keep up the pace without making mistakes. Just think about setting up 96 golden
| |
− | reactions
| |
− | with 8 parts each, including buffer and enzymes. This would result in 1056 single pipetting steps for a single
| |
− | 96 well plate!
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | Continuing down this path we proceeded by automating the transformation protocol using chemically competent
| |
− | cells and the Opentrons’ temperature module. An issue we encountered was the fast transition of the cells from
| |
− | low temperature to 42°C. We implemented the feedback of Keoni Gandall from Drew Endy’s lab in Stanford to
| |
− | pipet the cells rapidly from the cooling block to the temperatur module. This should yield in the highest
| |
− | transformation efficiency possible. We can now transform <i>E. coli</i> in a 96 well format at the same time.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | The next milestone on our way was to go from a full 96 well plate to colonies on an agar plate. We had to
| |
− | become
| |
− | a little bit more creative with that: plating every transformation on a single plate was not a valid option as
| |
− | it would limit our scale pretty quickly. Additionally it is up to date impossible to streak out liquids on an
| |
− | agar plate with the Opentrons, which is the manual way that transformations are spread. We decided to follow
| |
− | the
| |
− | advice of Keoni to do 4 dilutions for every transformation and plate all of them on 4 SBS one-well agar plates
| |
− | by spotting 1 µl in an 12x8 array. The higher the dilutions, the fewer cells are spotted per drop, eventually
| |
− | resulting in single colonies.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | After having single colonies on our SBS plates, we also implemented <a style="padding: 0"
| |
− | href="https://2019.igem.org/Team:Marburg/Colony_Picking">colony picking</a> and <a style="padding: 0"
| |
− | href="https://2019.igem.org/Team:Marburg/Miniprep">plasmid purification</a> to finish the whole construct
| |
− | building workflow.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | All these protocols for PCR reaction, Golden Gate assembly, transformation and plating are available with
| |
− | detailed documentation on <a style="padding: 0"
| |
− | href="https://github.com/igemsoftware2019/iGemMarburg2019">Github</a>, ready to
| |
− | be implemented by other iGEMs team that share our dream of the “lights-out-laboratory”.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | We know that we are not saving the world with automating single steps in cloning processes, but we think
| |
− | that these are some essential steps towards a future in which every iGEM team with an Opentrons robot can go
| |
− | to the next level of automation thanks to all our <a
| |
− | href="https://github.com/igemsoftware2019/iGemMarburg2019/tree/master/Hardware">hardware</a> and <a
| |
− | href="https://github.com/igemsoftware2019/iGemMarburg2019/tree/master/AI">software</a> solutions. Our
| |
− | vision is to free up their time to focus on designing even more awesome projects, achieving even greater
| |
− | results, dreaming even bigger dreams.
| |
− | </p>
| |
− | </article>
| |
− | </section>
| |
− | </div>
| |
− | <div style="margin-top: 10vh;">
| |
− | <center>
| |
− | <h1 class="title">G.U.I.D.E - Graphical User Interface for Directed Engineering</h1>
| |
− | </center>
| |
− | <section class="section">
| |
− | <article>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | A large part of the work that we as biologists do in the laboratory consists of repetitive, monotonous,
| |
− | mundane tasks. Imagine a world in which the scientist is liberated from these experiences and is able to fully
| |
− | concentrate on the important things of their project. Enter the world of automation. We firmly believe that
| |
− | affordable lab automation will fundamentally change the field of biology as we know it today. In order for
| |
− | this change to be a positive one, we consider it indispensable to take greater account of the end-user.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | Unfortunately, most of us had the experience that a great deal of software solutions in science are too
| |
− | difficult to use and therefore discourage many potential users from the get go.
| |
− | In order to tackle this problem, this year’s team has given a lot of thought into what makes a good user
| |
− | experience and how to use this to bring our automation efforts to a wider audience.
| |
− | Our project required a variety of Opentrons OT-2 protocols that range from simple dilution series to much more
| |
− | complex Golden Gate assemblies.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | To reconcile this diverse set of protocols without overwhelming the user, it requires intuitive software that
| |
− | packages modern features, such as drag and drop support, an easy to use deck overview and intelligently groups
| |
− | features that are more advanced.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | Fortunately, these ideas thoughts came around the same time as the invitation to the BioHackathon from <a href="https://2019.igem.org/Team:Vilnius-Lithuania/Public_Engagement">iGEM Vilnius</a>, allowing us to put them directly into practice.
| |
− | The Hackathon gave us the unique opportunity to discuss our efforts with other iGEM teams and experts from
| |
− | different disciplines, making it possible to immediately implement the feedback.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | We worked on an app were protocols can be integrated simply via drag and drop.
| |
− | After successfully loading the protocol into its library, the user can see not only the labware used, but also
| |
− | the liquids and their correct position on the OT-2 deck. Additionally the applications allows for protocol
| |
− | simulation, advanced code view and the change of variables
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | After just 3 days our prototype had many of the aforementioned features making the participation a resounding
| |
− | success. Later development allowed us to expand its functionality and smooth out its edges.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | The user interface (UI) is written in C# and can interface modified Opentrons protocols that are written in
| |
− | python via json files that define variables such as labware and liquids.
| |
− | In order to make the UI more visually appealing we designed multiple vector graphics of the labware and robot.
| |
− | </p>
| |
− | <p style="text-align: justify; margin-bottom: 1em;">
| |
− | We believe that this is a step in the right direction for a more user-friendly automation environment and hope
| |
− | to build upon this experience to expand this project in the upcoming years.
| |
− | </p>
| |
− | </article>
| |
− | </section>
| |
− | <hr>
| |
− | </div>
| |
− | </div>
| |
− | </body>
| |
| | | |
| </html> | | </html> |
| {{Marburg/footer}} | | {{Marburg/footer}} |