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Team:USTC Software/Features
From 2010.igem.org
Contents |
Fun and Function
MoDeL: Modeling Database Language
Bring Biological Modeling to the Next Level
| Chain-Node Model (Figure. 1) is a brand new Complex Modeling Concept incorporating its 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 consists of an arrangement of its basic unit, Part, whose concept has been greatly extended and includes but not limited to Biobrick Parts. The Node component is not a natural correspondence but 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 other nodes. However, parts or nodes in bound states are not allowed to bind again. With help of chains and nodes, it is possible to model any complex with arbitrary architecture. How wonderful it is!
One basic assumption of our model is that complex always inherits its parts’ properties. Though imprudent sometimes, this assumption greatly extend the usability of automatic modeling, with just a few parts, one can construct a bunch of complex with functions. |  |
| Binding in complex is characterized by connecting Nodes to form trees. It’s as simple as constructing a new node with bond nodes as its children. For example the binding structure of TetR dimer is considered as a TetR2 node with two TetR nodes as its children. Available nodes can be any part on a chain or even nodes of binding sites, which allows you to create a huge binding tree or even a forest of trees. Node makes the description of complicated binding in complex possible. | |
| Users are suggested to read this One-Minute Introduction to have an intuitive idea and deeper understanding of our modeling system. | |
Modeling with Templates
| Similar reactions happen for similar reasons. For example, the repression of pTetR promoter by TetR dimer can happen on many different DNA molecules with pTetR, regardless of what other biobricks is constructed on the DNA. With this thought, we add the part of Substituent, which can replace inactive parts of Species in Reactions, making it more general, and actually turning it into a reaction template. Having substituent, a pTetR TetR binding reaction is re-interpreted as the binding reaction of ANY DNA with pTetR(Figure 2) with ANY protein with TetR-dimer binding site. Modeling with templates allows us to describe reactions of new complex even without rewrite the reactions and species in database. |  |
Automatic Modeling Database Language
| We use a database to store all the information we need in modeling. In order to realize automatic modeling, we construct the database in unified format and make it machine-readable. Every component of database has its specified attributes and values, which makes the format of the database a unique yet 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. |  |
