Cooperation
We wanted to give something to the iGEM Community and help other teams as much as possible.
Seekers
From the start, we planned to develop software tools to make the work of our team easier. We also want to share the tools with the iGEM Community to help everyone.
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 Seekers for making background research for iGEM projects a little easier. They are both 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 code, so expanding the tools for the future only requires adding data.
Both use Yeoman for scaffolding and deployment and they are currently running on GitHub Pages, which is free and handles requests very fast, so they will stay available for the foreseeable future.
BioBrick Seeker
The major tools we made are the Seeker-brand tools. First we made BioBrick Seeker. 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 at the project's GitHub page.
Here's a screenshot of BioBrick Seeker and how it works if you want to search for a BioBrick that has the word 'fluorescent' in its description.
Team Seeker
The second seeker was Team Seeker, a tool to search through the project abstracts of past teams to see if something you've been thinking about has been done before and to find projects that work in a similar field to your own. It has a smart phrase search so 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 (linkki protokolla-PDFään).
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
Complexity survey (more than 20 entries) and Low Budget iGEM Challenge
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
Survey participation, 20 entries
Amsterdam 2012
Meetings with a PhD student Tania from University of Helsinki, plenty of advice and feedback about our pitch etc.
Groningen 2012
Skype call, getting to know to the factors what makes an iGEM project successful one
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