Team:Aalto-Helsinki/Cooperation

From 2014.igem.org

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     <h2>Seeker Tools</h2>
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         Right from the start, we decided that we were going to develop software tools to make the work of our team easier. We also wanted to share the tools with the iGEM Community to help everyone else, too!
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                Right from the start, we decided that we were going to develop software tools to make the work of our team easier. We also wanted to share the tools with the iGEM Community to help everyone else, too!
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        We made two different Seeker brand tools (BioBrick Seeker and Team Seeker) for making the research part of iGEM projects a little easier. Both have tens of thousands of lines of data to search through, but the results update in real-time. Both get their content from JSON files that can be easily added to and which are completely separate from the code, so expanding the tools for the future can be done by just adding new data!
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                We made two different Seeker brand tools (BioBrick Seeker and Team Seeker) for making the research part of iGEM projects a little easier. Both have tens of thousands of lines of data to search through, but the results update in real-time. Both get their content from JSON files that can be easily added to and which are completely separate from the code, so expanding the tools for the future can be done by just adding new data!
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        Both of the Seekers were written in JavaScript using the <a href="https://angularjs.org/">Angular.js</a> library. They use Yeoman for scaffolding and deployment, and they are currently running on GitHub Pages. GitHub Pages is a free service that handles requests very quickly, so the Seekers will stay available for the foreseeable future.
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                Both of the Seekers were written in JavaScript using the <a href="http://angularjs.org/">Angular.js</a> library. They use Yeoman for scaffolding and deployment, and they are currently running on GitHub Pages. GitHub Pages is a free service that handles requests very quickly, so the Seekers will stay available for the foreseeable future.
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        All of the code is available as open source on GitHub and is free to be reused, modified and expanded. All of our programming projects can be found through our GitHub organization <a href="http://github.com/iGEM-QSF">Quiet Sushi Force</a>.
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                All of the code is available as open source on GitHub and is free to be reused, modified and expanded. All of our programming projects can be found through our GitHub organization <a href="http://github.com/iGEM-QSF">Quiet Sushi Force</a>.
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            <blockquote>BioBrick Seeker has been used on 5 continents</blockquote>
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            <blockquote>BioBrick Seeker has been used on 5 continents</blockquote>
 
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Revision as of 11:01, 17 October 2014

Cooperation

How we helped the the iGEM community and how others helped us.

Scroll down to read more
Seeker Tools
Interlab Study
Interteam Cooperation

Photo © Tanja Maria

Seeker Tools

Right from the start, we decided that we were going to develop software tools to make the work of our team easier. We also wanted to share the tools with the iGEM Community to help everyone else, too!

We made two different Seeker brand tools (BioBrick Seeker and Team Seeker) for making the research part of iGEM projects a little easier. Both have tens of thousands of lines of data to search through, but the results update in real-time. Both get their content from JSON files that can be easily added to and which are completely separate from the code, so expanding the tools for the future can be done by just adding new data!

Both of the Seekers were written in JavaScript using the Angular.js library. They use Yeoman for scaffolding and deployment, and they are currently running on GitHub Pages. GitHub Pages is a free service that handles requests very quickly, so the Seekers will stay available for the foreseeable future.

All of the code is available as open source on GitHub and is free to be reused, modified and expanded. All of our programming projects can be found through our GitHub organization Quiet Sushi Force.

BioBrick Seeker has been used on 5 continents

BioBrick Seeker

BioBrick Seeker was created to make searching for the needed BioBricks in the 2014 iGEM Distribution a bit easier. It can be used to find Bricks with a certain keyword or list all from a certain type. It even has a search for the part names to see if the Brick you need is in this year's distribution.

All of the code and installation instructions for future development are available on the BioBrick Seeker GitHub page.

BioBrick Seeker Reception

The tool was received very well and got a lot of mentions on Twitter and got even featured on the iGEM 2014 Help page. We put Google Analytics on the site to get a rough idea of where in the world the tool was actually used. It turned out that it has been used on five different continents by many many teams all around the world!

BioBrick Seeker in action, searching for BioBricks that have the word 'fluorescent' in their description.

BioBrick Seeker has been used around the world! From this map you can see the of the amount of sessions from different countries: the darker blue, the more sessions there has been from the country. Picture taken on October 12th 2014.

Team Seeker

Team Seeker is a tool that you can use to search through the project abstracts of past teams. With this tool you don't need to use hours of research time to make sure that your idea hasn't been done yet in iGEM but you can just type in what you wish to find! With Team Seeker it's also easy to find all the projects that are close to your interests and this way the background research becomes a lot easier. Team Seeker has a smart phrase search; writing relevant phrases or words in the search bar brings up projects relating to them.

All of the code and installation instructions for future development are available at the project's GitHub page.

Looking for bioplastic worms with Team Seeker.

Interlab Study

We participated in the Measurement Interlab Study arranged by iGEM. Here are our results.

Devices We Used

  1. BBa_I20260 in pSB3K3 (sequencing data in a picture or text format)
  2. BBa_K823005 + BBa_E0240 in pSB1C3 (B0032-E0040-B0015) in pSB1C3 (sequencing data in a picture or text format)
  3. BBa_K823012 + BBa_E0240 (B0032-E0040-B0015) in pSB1C3 (sequencing data in a picture or text format)

Protocols

Building the Devices

We built the test devices with the same ligation protocol that we have used for all our ligations. The protocol can be found here (click).

Testing Protocol

The samples were grown in LB broth, in E. coli Top10 and they were incubated in 37 C° (shaker 220 rpm) for 17 hours. Before measuring the GFP levels, the samples were diluted to achieve the same OD600 and 100 ul of each sample was pipetted onto a 96-well black microtiter plate. We had three samples of all three devices.

The microtiter plate was inserted in a Thermo Scientific Varioskan and the following parameters were set:

  • Excitation wavelength: 470 nm
  • Emission wavelength: 511 nm
  • Bandwidth: 5nm
  • Measurement time: 500 ms

We used BBa_K592009 (in pSB1C3, grown in Top10) in LB, and LB only as negative controls. We didn’t have a positive control for these measurements.

Results

All measurement data () is in Relative Fluorescence Units (RFU).

. Measurement data.

Interteam Cooperation

ETH Zürich

Low Budget iGEM Challenge

We did some extraordinary intercountry collaboration with ETH Zürich team. Together we participated in the Low Budget iGEM Challenge arranged by Colombia's iGEM team. With ETH Zürich we planned, carried out and reported our experiments regarding an accessible, easy and low cost PCR method. You can find our entry from here. Furthermore, we made a video describing our method in more detail. You can find the video featuring Oskari from Aalto-Helsinki and Sumana from ETH Zürich below:

We participated in the Low Budget iGEM Challenge together with ETH Zürich! Click to watch the video.

Complexity Survey

ETH Zürich team investigated the emergence of complex patterns. We helped their human practice part by filling out their survey about how we perceive complexity in everyday life as in biology and its emergence and how we react to it. We shared the survey for our friends and collected responses on our Facebook page. As a result, we reached over 20 entries and received this awesome badge as a reward!

Here's the badge we earned for getting more than 20 entries for ETH-Zürich's complexity survey!

Colombia

We Skyped with Daniela from Colombia iGEM team and agreed on participating their human practices project, the Low Budget iGEM Challenge. We also discussed about her previous experiences and how they have done mathematical modeling in the previous years. This way, we could validate whether our approach to modeling was on the right track. It was very interesting to discuss about the differences in research and how it affects iGEM in Colombia. For example, ordering primers, kits or other materials takes a lot longer and it really limits the way of working there.

Minttu, Oskari and Pietu skyping to Columbia.

Paris-Saclay

Paris-Saclay was the first iGEM team we got to talk to. It was great to hear of people doing the same kind of thing, though it was also kind of intimidating with such a big group and many advisors. It seemed like we'd need more knowledge to pull this off. Being a Finnish team, we appropriately Skyped from a sauna-themed meeting room! We did wear clothes, though.

We got a lot of good tips about where to start, what to focus on and what to expect at Jamboree. They were doing bio art, so we contacted Aalto University's Biofilia (a biological art unit under the Aalto ARTS) for them. Biofilia were very interested in talking with the Paris-Saclay team about their "Ceci n'est pas un citron" project.

This is how Paris Saclay's team saw us during the Skype call.

Virginia

We participated in Virginia iGEM team's survey regarding synthetic biology. It was easier said than done, however. We wandered around Helsinki city centre looking for volunteers with time to answer the survey and offered buns and coffee as an exchange for their time. After a long day we finally reached over 20 responses!

This is the well deserved badge we received for reaching over 20 entries on Virginia's survey!

Amsterdam 2012

We were contacted by Tania Quirin via Facebook. She's from Amsterdam 2012 iGEM team and she's doing her PhD at University of Helsinki. We met Tania several times and got very valuable feedback about our work and presentation but also reflected our experiences to theirs.

Tania has been encouraging and supporting our team in so many ways and even came to see us on Summer of Startups Demo Day. She was the first iGEM alumna we actually met. She also connected us with iGEM-winning Groningen 2012 team's Arjan.

Groningen 2012

We had a long Skype call with Arjan Oldebesten from iGEM-winning Groningen 2012. We were very excited for this opportunity to hear about full scale iGEM experience including world championship Jamboree.

Trying to understand the factors for successful iGEM project, we discovered that success in iGEM does not require a huge amount of experience, top-notch facilities nor a mentor constantly guiding the team and its progress. They had a fairly simple, yet very interesting idea and they worked they way from bottom to top. They got the attitude, the hard work and the necessary support.

Based on these conversations, we think success in iGEM can be within our reach, too, even though we are the first Finnish team participating in iGEM! In fact, we believe that being the first team makes us look for advice from all over the world and brings a truly international feeling to the project.

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