Team:USTC Software/Features

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Revision as of 01:28, 21 October 2010

Overall project

One of the objectives of synthetic biology is the design and construction of new biological devices and systems to deliver useful applications. CAD (computer-aided design) tools, such as Tinker Cell, have been developed to model and simulate biological system and give its behavior as guides. However, they all need users to provide details of the system network, such as the activation and repression of transcription and translation reactions in genetic regulatory network. It is so difficult for even professionals to construct a detailed network of a complex system only depending on their minds. In this sense, modeling through CAD tools will not reduce the work of modeling: users are actually required to model manually and input their model in details. To solve this problem, we design a new method for automatic modeling: only (缺东西）assembling of parts and other initial environment parameters are needed for our program to discover the network from initial conditions and generate the model automatically. We believe this will greatly relieve users from complex interactions of species in biological system.

Our program is modular and has 3 major components. The first aspect is user interface (链接). Users could give their assembling of parts by drag-and-pull function and setup initial conditions as well. System behavior as output will also be shown there. The second aspect is a XML-based database. We propose a new language, MoDeL (System Biology Part Modeling Database Language),

MoDeL: Modeling Database Language

Bring Biological Modeling to the Next Level

Chain-Node Model (Figure. 1) is a brand new Complex Modeling Concept incorporating detailed structure description with universal applicability. Instead of treating complex as a whole while ignoring their basic composition and structure, Chain-Node Model view complex as a construction of it basic Parts. Just as its name implies, our model includes two components: Chain and Node. As a correspondence to natural polymer chains, each Chain is consisted of an arrangement of its basic unit, Part, whose concept has been greatly extended. Parts include but not limited to Biobrick Parts.	Figure 1: Logo of Chain-Node Model
The Node component does not have a natural correspondence. It is an abstract concept to describe binding states of two or more parts: each binding will create a Node. The abstract nodes may continue to bind with other parts or nodes to form a tree structure. However, parts or nodes in bound states are not allowed to bind again. With the help of chains and nodes, it is possible to model any complex with arbitrary architecture. Simple and inaccurate modeling of biological process could not keep pace with the development of synthetic biology and undoubtedly, our Chain-Node model provides a possible solution to the imbalance.
A simple example, tetR dimer, is shown to illustrate our simple modeling idea (做一个tetR2的模型放在右边做为配图，否则右边太空了). It has two chains with each containing only one part, tetR. Dimerization of tetR will create a node to indicate the bound state of two parts. To explain more clearly, bound parts are also considered as nodes so that in this example, all nodes are organized in a tree structure, which includes two children (leaf) nodes and one parent node. We will conform to this convention in our wiki.	Figure 1: Logo of Chain-Node Model
To know more, users are suggested to read this One-Minute Introduction to have an intuitive idea of our modeling system.

Modeling with Templates

Modeling manually of biological system is widely used for synthetic biology modeling but it requires an overall understanding of the biological network. It is difficult for even professionals to provide such large amount of data. The underlying reason making modeling so difficult is that the data provided manually are redundant because different reactions may occur through different mechanisms. Based on this. we are always seeking feasible ways to implement our automatic modeling idea. The automatic does not mean modeling without any information provided, but however, there indeed exists a minimal data set to enable the automation. The minimal data set is the Templates. Similar to C++ programming language, we introduce templates to allow generic description of species and reactions of a certain structural pattern or reaction mechanism. There are two kinds of templates: species templates and reaction templates. A template species behaves like species except that the template can have unknown parts of many different types. In other words, a species template represents a family of species. To apply this idea, we design a special part, ANY, of class Substituent, to represent unknown parts of any length on one chain. For example, a species with structure ANY - pTetR - ANY represents any species with part pTetR. A reaction template provides a specification for generating reactions with the same mechanism. Species in reaction templates are all templates, too. This could be understood more clearly by interpreting the known parts of species templates as the functional group -- a reaction template describes the interaction mechanism of these functional groups. For example (去做一个合适的example), pTetR promoter is deactivated in presence of TetR dimer which usually occupies the RNA polymerase binding site of pTetR sequence. The template species are pTetR template and TetR dimer template (see Figure) and the functional groups are pTetR promoter and TetR dimer. Any pair of species which partially contain pTetR DNA and TetR protein dimer respectively would bind according to the description of this reaction template. Modeling with templates allows users to define species and reactions only once for one certain family without rewriting them again in database.

Figure 2: Template of pTetR DNA

Automatic Modeling Database Language

The data used for automatic modeling should be well organized. For this purpose, we construct a database in unified format and make it machine-readable. Since everyone is allowed to add, delete or modify data stored in the database, each component of the database must be specified to a clear format, which defines a standard database language. We call it MoDeL: Modeling Database Language by picking out characters from three words. MoDeL is based on XML language, which makes it flexible and extensible. For more specifications of MoDeL, click here.	Figure 3: A peek at our database