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From 2010.igem.org

Contents 1 Language specifications 2 History(optional) 3 Future work 3.1 New version of MoDeL 3.2 New functions of 'iGame

Language specifications

History(optional)

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.