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From 2010.igem.org

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

MoDeL is young, to be exact, just born. There must be a long way before he can stand up and run by himself. At this stage, we have to take extra care of him. Knowing the drawbacks of MoDeL, we have already got a list of improvements waiting to be implemented in the next version of MoDeL. They are:
Enhance MoDeL to 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.

More powerful substituents.

• Only six kinds of substituents 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, and 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 that can provide enough information.

Enable description of transcription and translation reactions.

• Currently, transcription and translation are handled differently with other reactions. It is necessary to modify MoDeL to incorporate description of the two reactions.

Eliminate the inconsistencies.

• In the current version of MoDeL, a bunch of inconsistencies exist. For example, the identifiers of compartments follow different restrictions from other global identifiers, and some components’ attributes are required to be a certain value. These problems make MoDeL not so elegant when looking at details. Work must be done to improve its consistency.

Be more independent.

• Currently, some of MoDeL syntaxes are defined for specific algorithms of iGaME. Being a language for automatic modeling, cooperation with algorithm is reasonable. However, we believe there are too many compromises, thus causing a number of inconsistencies. In the next version, we are looking forward to a more independent MoDeL.

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.