From 2010.igem.org

Revision as of 18:44, 25 October 2010

Standardization of MoDeL

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 RFC 55 for MoDeL, and constructed a beta version of XML schema to describe the XML structure of MoDeL.

RFC 55

BBF RFC 55: 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 RFC 55 - Table of Contents

The document of RFC55 will soon be submitted. You can find it on the webpage of [http://openwetware.org/wiki/The_BioBricks_Foundation:RFC The BioBricks Foundation:RFC]. Following are some more previews at the draft document.

Figure 2: Preview at draft document of RFC 55

Figure 3: Preview at draft document of RFC 55

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 2: Preview at XML Schema of MoDeL

Figure 3: Preview at XML Schema of MoDeL

Future work

To promote MoDeL for wide use as a standard, we need to refine the structure of MoDeL definition and extend its content to enable descriptions of more biological process. In the future, the new version of MoDeL will be proposed and new functions of iGame will be added.

New version of MoDeL

Our beta version of MoDeL needs to be improved in several aspects. First, it does not support description of intra-molecular reactions. If it is applied, our software will become a useful tool to study the competition mechanism between intra-molecular and inter-molecular reactions. Second, only six kinds of substituent parts are far from meeting the demands of more accurate modeling and complex reaction mechanism. At present, substituent parts are limited to match only parts on one chain; they are not allowed to represent a structure with more than one chains and trees. This needs the extension of definition of substituent parts by designing a unified format with enough information. Third, transcription and translation reactions are handled differently with other reactions. It is necessary to modify MoDeL to incorporate description of transcription and translation reactions.

New functions of 'iGame

There are also some points that are needed to be improved for iGame. First, it is far from enough to provide dynamic curves as output because users may not care about them. They want to know the network, which consists of species and reactions. We have planned to give a graphic display of the system network by showing the change of quantities and directions of species dynamically. Users could understand the underlying reasons why a curve reaches its peak from the network. Second, graphical tools for creating, removing, modifying data in database are also needed. It will greatly reduce the difficulty for users to construct their own database. In addition, function of format-checking for data written in MoDeL will also be added in the future.