Team:Sevilla/Project/ubbit

From 2011.igem.org

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We propose the widening of the BioBrick standard, not by increasing the library of components but adding steps in the abstraction hierarchy. We believe that the tendency of synthetic biology in this decade is going to be the distribution of complex functions among strains so that the cells are not overloaded. The rise of the number of communication substances  will limit the number of strains that can remain in the same environment.That leaves us with the necessity of dividing physically the strains in different places. This project pursues the objective of finding a substance that acts as a link among communities, thus becoming a putative synthetic quorum sensing system. This substance, the Universal BioBit (Ubbit) shall fulfill certain requirements: firstly, biosynthesis should be possible; secondly, it needs to be degraded efficiently; and thirdly, it should induce the genetic expression of what we want in a target cell. Our research will assess the behavior of many substances and finally we will publish the results with a free use license (probably Creative Commons).
We propose the widening of the BioBrick standard, not by increasing the library of components but adding steps in the abstraction hierarchy. We believe that the tendency of synthetic biology in this decade is going to be the distribution of complex functions among strains so that the cells are not overloaded. The rise of the number of communication substances  will limit the number of strains that can remain in the same environment.That leaves us with the necessity of dividing physically the strains in different places. This project pursues the objective of finding a substance that acts as a link among communities, thus becoming a putative synthetic quorum sensing system. This substance, the Universal BioBit (Ubbit) shall fulfill certain requirements: firstly, biosynthesis should be possible; secondly, it needs to be degraded efficiently; and thirdly, it should induce the genetic expression of what we want in a target cell. Our research will assess the behavior of many substances and finally we will publish the results with a free use license (probably Creative Commons).
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====The Ubbit and its practical use in biodevice design====
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      <p>The Ubbit and its practical use in biodevice design</p>
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In order to understand and apply this standard, a definition of new theoretical concepts is needed.  
In order to understand and apply this standard, a definition of new theoretical concepts is needed.  
Firstly, a community is built with different strains (prokaryotic or eukaryotic) exchanging information between them so that the whole community can perform a specific function. The information would probably be of a chemical nature, like the AHLs used by bacteria for the quorum sensing, though we don’t reject other kinds of data (one of the iGEM contestant teams has recently suggested using light as a way of information transmision). We define any substance (or non-molecular analogue) that acts as data for a couple of cells as BioBit or bbit. In a community we’ll have input and output bbits besides the internal communication bbits. In order to implement the Ubbit standard, a community will have to emit output bbits that can be detected as input information by another cell or group of cells, and induce a differential gene expression in them, so that they can bio-synthetize new outputs bbits for the next cell. So, if a community had three input bbits (a, b and c), it would need three modified strains, named translators, that could synthetize each substance when detecting Ubbit. With the substances emited by the community after receiving the input information it would happen the other way round; if the community produces two bbits (d and e) there will be two strains that could specifically transform each of the outputs bbits into Ubbit.
Firstly, a community is built with different strains (prokaryotic or eukaryotic) exchanging information between them so that the whole community can perform a specific function. The information would probably be of a chemical nature, like the AHLs used by bacteria for the quorum sensing, though we don’t reject other kinds of data (one of the iGEM contestant teams has recently suggested using light as a way of information transmision). We define any substance (or non-molecular analogue) that acts as data for a couple of cells as BioBit or bbit. In a community we’ll have input and output bbits besides the internal communication bbits. In order to implement the Ubbit standard, a community will have to emit output bbits that can be detected as input information by another cell or group of cells, and induce a differential gene expression in them, so that they can bio-synthetize new outputs bbits for the next cell. So, if a community had three input bbits (a, b and c), it would need three modified strains, named translators, that could synthetize each substance when detecting Ubbit. With the substances emited by the community after receiving the input information it would happen the other way round; if the community produces two bbits (d and e) there will be two strains that could specifically transform each of the outputs bbits into Ubbit.
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The community would be held in a physical stand; the community along with its translator strains and the physical medium would constitute what we call module. The modules would be as little black boxes of which we only know their behaviour; their inputs, outputs and the function they perform. They would be ready to be connected to modules created by other bioengineers. Then we would have a population, a network of interconnected modules exchanging information in Ubbits.
The community would be held in a physical stand; the community along with its translator strains and the physical medium would constitute what we call module. The modules would be as little black boxes of which we only know their behaviour; their inputs, outputs and the function they perform. They would be ready to be connected to modules created by other bioengineers. Then we would have a population, a network of interconnected modules exchanging information in Ubbits.
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====The new levels of abstraction====
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We propose the following ones:
We propose the following ones:
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#Population Level, in which the whole community works to do the logical functions, exchanging Ubbits as data. We talk about population computers.
#Population Level, in which the whole community works to do the logical functions, exchanging Ubbits as data. We talk about population computers.
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====The Ubbit standard beyond the iGEM: Ubbit.com====
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      <p>The Ubbit standard beyond the iGEM: Ubbit.com</p>
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All these new rules for the different levels of abstraction will make up the Ubbit Standard. Although at first the idea of entering the competition was the main driving force, day by day we’re growing more and more convinced that the Ubbit Standard could (and even should) stay alive after the iGEM, and we’re becoming to look at the competition as a unique opportunity to promote our idea. We have already bought the rights to create a web site, Ubbit.org, that is mean to become the first database of complex synthetic bio-devices. In this web all the models that comply with the conditions of the Ubbit Standard, described by researchers all over the world, would be stored and could become accesible, with the appropriate licences (probably Creative Commons). Besides, it would be the place to give references and look up the standard’s rules, as well as the possible updatings and extensions. We’ll try to promote the site and its content as a natural extension of the iGEM BioBrick Standard developed by Knight, Endy and Voigt. This would place our university, the University of Seville, our city and our country, among the pioneer institutions in the area of synthetic biology.
All these new rules for the different levels of abstraction will make up the Ubbit Standard. Although at first the idea of entering the competition was the main driving force, day by day we’re growing more and more convinced that the Ubbit Standard could (and even should) stay alive after the iGEM, and we’re becoming to look at the competition as a unique opportunity to promote our idea. We have already bought the rights to create a web site, Ubbit.org, that is mean to become the first database of complex synthetic bio-devices. In this web all the models that comply with the conditions of the Ubbit Standard, described by researchers all over the world, would be stored and could become accesible, with the appropriate licences (probably Creative Commons). Besides, it would be the place to give references and look up the standard’s rules, as well as the possible updatings and extensions. We’ll try to promote the site and its content as a natural extension of the iGEM BioBrick Standard developed by Knight, Endy and Voigt. This would place our university, the University of Seville, our city and our country, among the pioneer institutions in the area of synthetic biology.
If you want to know more of Ubbit.com, visit the corresponding [[2011.igem.org/Team:Sevilla/Software/Ubbit|wiki section]].
If you want to know more of Ubbit.com, visit the corresponding [[2011.igem.org/Team:Sevilla/Software/Ubbit|wiki section]].

Revision as of 10:25, 20 September 2011





We propose the widening of the BioBrick standard, not by increasing the library of components but adding steps in the abstraction hierarchy. We believe that the tendency of synthetic biology in this decade is going to be the distribution of complex functions among strains so that the cells are not overloaded. The rise of the number of communication substances will limit the number of strains that can remain in the same environment.That leaves us with the necessity of dividing physically the strains in different places. This project pursues the objective of finding a substance that acts as a link among communities, thus becoming a putative synthetic quorum sensing system. This substance, the Universal BioBit (Ubbit) shall fulfill certain requirements: firstly, biosynthesis should be possible; secondly, it needs to be degraded efficiently; and thirdly, it should induce the genetic expression of what we want in a target cell. Our research will assess the behavior of many substances and finally we will publish the results with a free use license (probably Creative Commons).

The Ubbit and its practical use in biodevice design


In order to understand and apply this standard, a definition of new theoretical concepts is needed. Firstly, a community is built with different strains (prokaryotic or eukaryotic) exchanging information between them so that the whole community can perform a specific function. The information would probably be of a chemical nature, like the AHLs used by bacteria for the quorum sensing, though we don’t reject other kinds of data (one of the iGEM contestant teams has recently suggested using light as a way of information transmision). We define any substance (or non-molecular analogue) that acts as data for a couple of cells as BioBit or bbit. In a community we’ll have input and output bbits besides the internal communication bbits. In order to implement the Ubbit standard, a community will have to emit output bbits that can be detected as input information by another cell or group of cells, and induce a differential gene expression in them, so that they can bio-synthetize new outputs bbits for the next cell. So, if a community had three input bbits (a, b and c), it would need three modified strains, named translators, that could synthetize each substance when detecting Ubbit. With the substances emited by the community after receiving the input information it would happen the other way round; if the community produces two bbits (d and e) there will be two strains that could specifically transform each of the outputs bbits into Ubbit.

The community would be held in a physical stand; the community along with its translator strains and the physical medium would constitute what we call module. The modules would be as little black boxes of which we only know their behaviour; their inputs, outputs and the function they perform. They would be ready to be connected to modules created by other bioengineers. Then we would have a population, a network of interconnected modules exchanging information in Ubbits.


The new levels of abstraction


We propose the following ones:

  1. Cell or Strain Level, in which the logical functions are carried out by sub-cellular components. We’re talking about cell or strain computers. At this level of abstraction is where the BioBrick standard plays its main role, though we will propose a much more potent, practical definition of the level.
  2. Community Level. Here, the strains are the ones who carry out the logical functions. We now talk about community computers.
  3. Population Level, in which the whole community works to do the logical functions, exchanging Ubbits as data. We talk about population computers.


The Ubbit standard beyond the iGEM: Ubbit.com



All these new rules for the different levels of abstraction will make up the Ubbit Standard. Although at first the idea of entering the competition was the main driving force, day by day we’re growing more and more convinced that the Ubbit Standard could (and even should) stay alive after the iGEM, and we’re becoming to look at the competition as a unique opportunity to promote our idea. We have already bought the rights to create a web site, Ubbit.org, that is mean to become the first database of complex synthetic bio-devices. In this web all the models that comply with the conditions of the Ubbit Standard, described by researchers all over the world, would be stored and could become accesible, with the appropriate licences (probably Creative Commons). Besides, it would be the place to give references and look up the standard’s rules, as well as the possible updatings and extensions. We’ll try to promote the site and its content as a natural extension of the iGEM BioBrick Standard developed by Knight, Endy and Voigt. This would place our university, the University of Seville, our city and our country, among the pioneer institutions in the area of synthetic biology.

If you want to know more of Ubbit.com, visit the corresponding wiki section.

Retrieved from "http://2011.igem.org/Team:Sevilla/Project/ubbit"