Edinburgh/DivisionPopper/SBApproach
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| - | '''MENU''' :[[Edinburgh/DivisionPopper| Introduction]] | [[Edinburgh/DivisionPopper/References|Background]] | [[Edinburgh/DivisionPopper/Applications|Applications]] | [[Edinburgh/DivisionPopper/Design|Design]] | [[Edinburgh/DivisionPopper/Modelling|Modelling]] | [[Edinburgh/DivisionPopper/Status| | + | '''MENU''' :[[Edinburgh/DivisionPopper| Introduction]] | [[Edinburgh/DivisionPopper/References|Background]] | [[Edinburgh/DivisionPopper/Applications|Applications]] | [[Edinburgh/DivisionPopper/Design|Design&Implementation]] | [[Edinburgh/DivisionPopper/Modelling|Modelling]] | [[Edinburgh/DivisionPopper/Status|Wet Lab]] | [[Edinburgh/DivisionPopper/SBApproach|Synthetic Biology Approach]] | [[Edinburgh/DivisionPopper/Conclusions|Conclusions]] |
Our team thinks of iGEM as a competition with two goals: the design and construction of a genetically engineered machine that proves to be useful and the investigation and innovation of the Synthetic Biology theoretical and practical tools. | Our team thinks of iGEM as a competition with two goals: the design and construction of a genetically engineered machine that proves to be useful and the investigation and innovation of the Synthetic Biology theoretical and practical tools. | ||
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== Synthetic Biology Approach == | == Synthetic Biology Approach == | ||
| - | Synthetic Biology aims to bring engineering approaches into the complex task of biochemical system modifications. We explain here our application of some | + | Synthetic Biology aims to bring engineering approaches into the complex task of biochemical system modifications. We explain here our application of some fundamental concepts: abstraction, decoupling, standards, compositionality, project management. |
=== Abstraction === | === Abstraction === | ||
| - | The abstraction hierachy is used to deal with the complexity of systems by selecting at each level only the | + | The abstraction hierachy is used to deal with the complexity of systems by selecting at each level only the meaningful characteristics, avoiding details from the other levels. We considered three different views of the Division PoPper: Device, Parts and DNA. The views are available in the section [[Edinburgh/DivisionPopper/Design|Design&Implementation]]. Since the Division PoPper is a device, the System view has been used to represent the composition of the device with other devices, in section [[Edinburgh/DivisionPopper/Applications|Applications]]. |
=== Decoupling === | === Decoupling === | ||
| - | We applied decoupling | + | We applied decoupling techniques by separating the phases of Design and Implementation. In particular in our case the decoupling has been almost natural in creating two different views of the Part abstraction level: the logic and biological view. As you can see in section [[Edinburgh/DivisionPopper/Design|Design&Implementation]], the logic view presents the functional elements of the device without mapping them to real biological elements, but just explaining the characteristics they should have in order to work. |
| - | The biological view is thus a possible implementation of the logic view, in which each functional element has been replaced by a real biological entity. Practically, in our group the logic view has been realized by group members with an engineering background, then has | + | The biological view is thus a possible implementation of the logic view, in which each functional element has been replaced by a real biological entity. Practically, in our group the logic view has been realized by group members with an engineering background, then has been passed to the members with a biology background for the selection of the more adapt implementation. Without aiming to make a general statement, we think that the decoupling between design and realization finds a natural interface at the level of parts. It seems to be the level of abstraction in which (at least for our group) the knowledge from different scientific backgrounds is more in contact. |
=== Standards === | === Standards === | ||
| - | In Synthetic Biology the concept of Standards is | + | In Synthetic Biology the concept of Standards is very important and can be applied in different aspects: in terms of signals, in terms of notations, in terms of biological constructs and so on. When possible, we tried to follow the official or de-facto standards. We designed a device with output in the form of PoPS signal in order to facilitate combination with other devices. We put in the form of BioBricks all the biological functional elements we used. In the diagrams of abstraction level views we used the shapes present in the Registry of Standard Biological Parts. |
=== Compositionality === | === Compositionality === | ||
| - | The decision of selecting a device as project, instead of a full system, has been driven by our | + | The decision of selecting a device as project, instead of a full system, has been driven by our desire to contribute to a further expansions of the Synthetic Biology library. In order to prove the compositionality property, we developed a mathematical model of our device when put in collaboration with an already existing device (a counter). Details in the [[Edinburgh/DivisionPopper/Modelling|Modelling]] section. |
=== Project Management === | === Project Management === | ||
| - | We divided the project work | + | We divided the project work into different phases and then associated team members to phases in order to distribute the work load. |
| - | [[Image:Projectmanagement.png| | + | [[Image:Projectmanagement.png|400px]] |
== Investigating Innovations == | == Investigating Innovations == | ||
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=== Stochastic Modelling with Process Algebras === | === Stochastic Modelling with Process Algebras === | ||
| - | Modelling, and in general mathematical and computational techniques, will be more and more | + | Modelling, and in general mathematical and computational techniques, will be of more and more help in Synthetic Biology. Although the modelling tools usually applied to Biology and Systems Biology seem quite well equiped for Synthetic Biology, there is of course the need to investigate more specialized tools. In particular we propose a little model using Stochastic Process Algebra, formal languages that have been proposed in the last five years in the field of biochemical simulations ([[Edinburgh/DivisionPopper/Modelling|Modelling]] section). We used the process algebra [http://www.dcs.ed.ac.uk/pepa/ PEPA], developed at Edinburgh University. |
| - | === Representing biological processes with standard graphical | + | === Representing biological processes with standard graphical notation === |
| - | + | Because biological processes are complex, it is usually quite difficult to explain them in a precise, intuitive and concise form. In order to solve this problem, some Standard Graphical Notations for biochemical systems have been proposed in the last year. In order to investigate the use of this notation for explaining Synthetic Biology construct processes, we created two [http://www.bioinformatics.ed.ac.uk/epe/ EPN (Edinburgh Pathway Notation)] diagrams that can be seen in the [[Edinburgh/DivisionPopper/Design|Design&Implementation]] section. EPN is one of the standards that are being considered in developing the new generation of [http://sbgn.org/ Systems Biology Graphical Notation (SBGN)]. | |
Latest revision as of 20:57, 26 October 2007
MENU : Introduction | Background | Applications | Design&Implementation | Modelling | Wet Lab | Synthetic Biology Approach | Conclusions
Our team thinks of iGEM as a competition with two goals: the design and construction of a genetically engineered machine that proves to be useful and the investigation and innovation of the Synthetic Biology theoretical and practical tools. Because of that, we spent as much attention and time in applying the Synthetic Biology paradigms and guidelines as in selecting and developing the actual construct. Since Synthetic Biology is a complex but quite new field of research, we think that even a group of undergraduate/graduate students working for two months on the project can help in investigating small innovations or improving the standard approach. In this section we explain the work we did in this direction.
Contents |
Synthetic Biology Approach
Synthetic Biology aims to bring engineering approaches into the complex task of biochemical system modifications. We explain here our application of some fundamental concepts: abstraction, decoupling, standards, compositionality, project management.
Abstraction
The abstraction hierachy is used to deal with the complexity of systems by selecting at each level only the meaningful characteristics, avoiding details from the other levels. We considered three different views of the Division PoPper: Device, Parts and DNA. The views are available in the section Design&Implementation. Since the Division PoPper is a device, the System view has been used to represent the composition of the device with other devices, in section Applications.
Decoupling
We applied decoupling techniques by separating the phases of Design and Implementation. In particular in our case the decoupling has been almost natural in creating two different views of the Part abstraction level: the logic and biological view. As you can see in section Design&Implementation, the logic view presents the functional elements of the device without mapping them to real biological elements, but just explaining the characteristics they should have in order to work. The biological view is thus a possible implementation of the logic view, in which each functional element has been replaced by a real biological entity. Practically, in our group the logic view has been realized by group members with an engineering background, then has been passed to the members with a biology background for the selection of the more adapt implementation. Without aiming to make a general statement, we think that the decoupling between design and realization finds a natural interface at the level of parts. It seems to be the level of abstraction in which (at least for our group) the knowledge from different scientific backgrounds is more in contact.
Standards
In Synthetic Biology the concept of Standards is very important and can be applied in different aspects: in terms of signals, in terms of notations, in terms of biological constructs and so on. When possible, we tried to follow the official or de-facto standards. We designed a device with output in the form of PoPS signal in order to facilitate combination with other devices. We put in the form of BioBricks all the biological functional elements we used. In the diagrams of abstraction level views we used the shapes present in the Registry of Standard Biological Parts.
Compositionality
The decision of selecting a device as project, instead of a full system, has been driven by our desire to contribute to a further expansions of the Synthetic Biology library. In order to prove the compositionality property, we developed a mathematical model of our device when put in collaboration with an already existing device (a counter). Details in the Modelling section.
Project Management
We divided the project work into different phases and then associated team members to phases in order to distribute the work load.
Investigating Innovations
When possible, we tried to investigate new tools related to the Synthetic Biology world.
Stochastic Modelling with Process Algebras
Modelling, and in general mathematical and computational techniques, will be of more and more help in Synthetic Biology. Although the modelling tools usually applied to Biology and Systems Biology seem quite well equiped for Synthetic Biology, there is of course the need to investigate more specialized tools. In particular we propose a little model using Stochastic Process Algebra, formal languages that have been proposed in the last five years in the field of biochemical simulations (Modelling section). We used the process algebra [http://www.dcs.ed.ac.uk/pepa/ PEPA], developed at Edinburgh University.
Representing biological processes with standard graphical notation
Because biological processes are complex, it is usually quite difficult to explain them in a precise, intuitive and concise form. In order to solve this problem, some Standard Graphical Notations for biochemical systems have been proposed in the last year. In order to investigate the use of this notation for explaining Synthetic Biology construct processes, we created two [http://www.bioinformatics.ed.ac.uk/epe/ EPN (Edinburgh Pathway Notation)] diagrams that can be seen in the Design&Implementation section. EPN is one of the standards that are being considered in developing the new generation of [http://sbgn.org/ Systems Biology Graphical Notation (SBGN)].
