SIP Wiki Analyser

Our first aim was to determine who will be the winner of the igem competition, analysing the wikis, finding original words, cooperative words or paper's lab words. Unfortunately, we didn't have time to make that, but we find that SIP characterize very well wiki, and find some original words.

We have calculate SIP words for each team and each year since 2007 using SIP.C, for each them we have take the 25 top sip valued words. We use TOP_SIP.C to make that, this software see what is the hight SIP value and then take N words with this hight SIP. When we got our words, we put in a [http://www.wordle.net/ software], to display them with graphical effect : words with hight frequencies has a big font, and words with low frequencies has a small font.

Paris 2007

First, we analyse the [http://parts.mit.edu/igem07/index.php/Paris team Paris 2007] and we get that (we have selected 60 words to get, with a filter : all words like "p1", "f23" are removed) :

You can see some gene displayed on the screen, which characterize the project :

• smb : the name of the project.
• cre/lox/lox66/DGAT/dapA etc. name of recomination site, molecules and genes, characterize their project.

"The aim of our project is to engineer the first synthetic multicellular bacterium, the SMB. This new organism is a novel tool for the engineering of complex biological systems. It consists in two interdependent cell lines. The first, dedicated to reproduction is the germ line (red cells in the simulation below). It is able to differentiate into the second line: the soma (green cells), which is sterile and dedicated to support the germ line. The germ line is auxotroph for DAP (diaminopimelate) which is provided by the soma. There is thus an interdependency relationship. The soma, being sterile, requires the germ line for its generation, while the germ line needs the soma to complement its auxotrophy. We provide here both experimental and computational evidences that this system can work, as well as the almost complete construction of the SMB."

Paris 2009

Then I try with Paris 2009 (for 25 words) :

I find OMV (outer membrane vesicles), ClyA, but you can also find words that it's possible, you don't understand, like : mardi, avoir, bien, avec. In fact these words are french words, very common french words (translation for each is tuesday, have, good, with) so SIP put them here, because it's french words, only this team used these terms, and because they are common in french language, they have a big frequence in the text.

Subject of the project Paris 2009 was :

"Message in a Bubble: a robust inter-cellular communication system based on outer membrane vesicles. Sending a message across the ocean… Outer membrane vesicles (OMV), naturally produced by gram negative bacteria such as E. Coli, are strong candidates for long-distance messaging. Our engineered communication platform consists in controlling OMV production by destabilizing membrane integrity through over-expression of specific periplasmic proteins (e.g. TolR). In order to control and modulate message content, we used fusions with OmpA signal sequence and the ClyA hemolysin as delivery tags. A targeting system was developed, based on the outer-membrane expression of Jun/Fos leucine zippers to control the vesicle flux between donor and recipient cells. Once received, the signal from incoming vesicles is transduced through a modified Fec pathway, whereby the receptor is provided by the OMV. Computational models provided insight to all of the above steps. Such reliable communications systems have wide biotechnological implications, ranging from targeted drugs delivery and detoxification to advanced division of labor or even cell-based computing. "

iGEM Winner