Edinburgh/DivisionPopper/SBApproach

From 2007.igem.org

Revision as of 15:18, 21 September 2007

MENU : Introduction | Background | Applications | Design | Modelling | Status | 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.

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 fundamentals concepts: abstraction, decoupling, standards, compositionality, project managing.

Abstraction

The abstraction hierachy is used to deal with the complexity of systems by selecting at each level only the meaningul characteristic, avoiding details from the other levels. We created three different views of the Division PoPper: Device, Parts and DNA. The views are available in the section Design&Realization. Since the Division PoPper is a device, the System view have been used to represent the composition of the device with other devices, in section Applications.

Decoupling

We applied decoupling techinques 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&Realization, 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 The biological view is thus a possible implementation of the logic view, in which each functional element has been replaced by a real biological entity.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 benn passed to the members with a biology background for the selection of the more adapt implementation. Without the aim to be 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 background are more in contact.

Standards

In Synthetic Biology the concept of Standards is really 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 composition with other devices. We put in 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 Parts.

Compositionality

The decision of selecting a device as project, instead of a full system, has been driven by our willing of contribute to a further expansions of Synthetic Biology library. In order to prove the compositionality property, we developed the 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 in 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 more and more of help in Synthetic Biology. Despite the modelling tools usually applied to Biology and Systems Biology seem quite well equiped for Syntehtic Biology, there is of course the need of investigating more specialized . 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 notations

Becuase biological processes are complex, it is usually quite difficult their explanation 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&Realization section. EPN is one of the standards that are considered in developing the new generation of [http://sbgn.org/ Systems Biology Graphical Notation (SBGN)].