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Cooperation

We wanted to give something to the iGEM Community and help other teams as much as possible.

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Seeker tools
Interlab Study
Interteam Cooperation

Photo © Tanja Maria

Seekers

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, too!

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

We made two different Seeker brand tools (BioBrick Seeker and Team Seeker) for making the research part of iGEM projects a little easier. Both of the Seekers were written in JavaScript using the Angular.js library. The data in both is a massive JSON file that is easily modifiable and can be changed without doing any modifications to the rest of the code: expanding the tools for the future only requires adding data!

Both Seekers use Yeoman for scaffolding and deployment, and they are currently running on GitHub Pages. GitHub Pages is free and handles requests very fast, so they will stay available for the foreseeable future.

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 are available on the BioBrick Seeker GitHub page.

Here's a screenshot of BioBrick Seeker and how it works if you want to search for BioBricks that have the word 'fluorescent' in their description.

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 anything in the search bar should bring up what you need.

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

Here's a screenshot of Team Seeker.

Interlab Study

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

Devices Used:

BBa_I20260 in pSB3K3
BBa_K823005 + BBa_E0240 in pSB1C3 (B0032-E0040-B0015) in pSB1C3
BBa_K823012 + BBa_E0240 (B0032-E0040-B0015) in pSB1C3

We sequenced all three devices and they were confirmed to be ok. You cand find the sequencing results by clicking the name of the device. (sekvenssitiedostot partsien nimiin, kuva/teksti?)

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 (table 1) is in Relative Fluorescence Units (RFU).

Table 1. Measurement data.

Interteam Cooperation

ETH Zürich

Low Budget iGEM Challenge

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

Complexity Survey

(more than 20 entries)

This is the badge we got for getting more than 20 entries for ETH-Zürich's survey!

Colombia

Mathematical modeling Low Budget iGEM Challenge entry

Minttu, Oskari and Pietu skyping to Columbia.

Paris-Saclay

Skype call, receiving the advice, first contact to iGEM seniors, Bioart collaboration to Finland

Virginia

Virginia's Survey