Team:USTC Software/modelStandardization


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Standardization of MoDeL

Ustcs Notepad edited 2.jpg

MoDeL aims at providing a language and syntax standard for automatic modeling databases used in synthetic biology models. Knowing the importance, USTC_Software puts a lot of effort on the standardization of MoDeL. We have requested BBF RFC55 for MoDeL, and constructed a beta version of XML schema to describe the XML structure of MoDeL.


BBF RFC55: Standard Biological Part Automatic Modeling Database Language (MoDeL) mainly describes the detailed language specifications of MoDeL with concrete examples, which provides enough information for serious database constructors to build up a database on his own. As a highlight of MoDeL, the concept and the syntax of Chain-Node Model are described in detail. The content of document is currently arranged as follows:

Figure 1: Draft document of RFC55 - Table of Contents

The document of RFC55 has already been submitted. You can find it on the webpage of The BioBricks Foundation:RFC. Following are some more previews at the draft document.

Figure 2: Preview at draft document of RFC55
Figure 3: Preview at draft document of RFC55

XML Schema

XML Schemas express shared vocabularies and allow machines to carry out rules made by people. They provide a means for defining the structure, content and semantics of XML documents. Being written in XML fashion, a Schema is perfect for MoDeL to allow software to perform check on syntax. Following is the preview of the beta version of XML Schema for MoDeL. The Schema can be downloaded at iGaME project page on SourceForge.

Figure 4: Preview at XML Schema of MoDeL
Figure 5: Preview at XML Schema of MoDeL