Team:METU-BIN Ankara/Collaborations


Revision as of 00:11, 22 September 2011 by Gngr (Talk | contribs)

METU-BIN iGEM Software TeamProject: Mining for BioBricks


Our software, M4B: Mining for BioBricks, is available for everyone, you can find us on the Community Page soon!


Since M4B contains bioparts from 2011 distribution in its database and we know METU-Ankara Team who are engineering E.Coli to decrease harmful effects of methane gas use 2011 distribution as well, we sent it them.

Their feedback is the following.

Click on the image to view larger size.

"We are constructing a device that is induced by IPTG and that gives lysis enzymes and GFP as the outputs because, in order to elute methanol we need to kill our modified cells that convert ambient methane to methanol and the reason why we want GFP as one output is to be sure that it works. Our modelled device has promoter induced by IPTG, RBS, gene coding GFP and lysis cassette ending with cell death and we are glad to have it and it's working how we expected. So then, we use M4B to see that if it finds the exact device or the device that can do the same job. Since the software has only one place for output, we queried IPTG as an input and GFP as an output on the software and got corresponding 117 results. These results contain devices exactly what we have one for the same operation. However, we couldn't find the lysozyme output for the IPTG input in the software."

We are pleased to hear the feedback of METU-Ankara Team and it's good the know that their first query on our software was successful. As for the second one, we haven't included DNA, RNA and tags yet. It's one of our future plans and next year, it'll be done. Furthermore, queries with multiple inputs or outputs will be available. So, in one operation, they will be able to get what they want. See our future plans on the next version.


We also collaborated with the team Uppsala-Sweden. Below, you can see their feedback on our project, the software: M4B: Mining for BİoBrick.

"The METU-BIN_Ankara team provided us their software which they developed for their project to test it if we can use for our Project. We examined the software by searching the parts that have been used during our Project.We used red,blue and green lights as input which activate red sensor(cph8), green sensor(ccaS) and blue sensor(YF1). We are aiming to get three colours as output which are blue output(amilCP), red output(mCherry) and green/yellow output(amilGFP).

However, we got no result for our specific input - output relations but, the software has some of the inputs and outputs.

This software is very helpful to search the parts and check if the parts are in the standart registry database and decide which parts work effectively with eachother as well.That provides an easy start to constract the parts and give more efficient results.

We appreciate METU-BIN_Ankara team to create that software and believe that it will be a very helpful software which will solve the problems that we or another teams faced up in the beginning.

The software can be improved further by adding more parameters."

We are happy to see that they use and have positive expressions on our software. As we got the information about their project, they are adding some of the bioparts of their modified device newly into the Registry. Because of this, and since our software has 2011 spring distribution in its database, it's normal to get no results for their specific device. However, when they'll add them and our database is updated, finally our software will be able to find that specific result.

At the same time, our team has given a feedback on the Biosafety document of the team Uppsala-Sweden, you can read it on this page.