Team:USTC Software/model future


Future work

Ustcs The-future.jpg

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.

Next 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

iGaME grows together with MoDeL. In the one-year process of software development, we have achieved many of our goals, and found even more to be achieved. Looking ahead, we have the following wishes for iGaME.

User-friendly output for both professionals and amateurs.

  • It is far from enough to provide only dynamic curves as output because users may want more information about the biological system. Professionals may want to know the whole picture of reaction network, how do the species react with each other, and what influence do they have on the network. Amateurs may not be interested in curves, and they want to have a more straightforward concept of the network.

We are planning to give a graphic display of the reaction network by showing the change of species quantities dynamically. Users could understand the underlying reasons why a curve reaches its peak from the network. We also plan to show the topological structure of reactions in network. By connecting species with reactions, users can get a clear picture of the interconnections between species.
User-friendly input with fun

  • Powered by MoDeL, iGaME has already relieved users from inputting massive amount of data. However, we are still looking forward to make the input process more fun. Besides providing a graphical scene, we are planning to have more elements like story telling and character selecting. Moreover, result grading and multi-user interacting are to be added to make our software a real game.

Database Development Kit

  • Though we have presented the detail document of RFC 55 for MoDeL, modelers may still found it a tough job to construct a usable database. The Database Development Kit aims at aiding modelers with easy-to-use development tools. To achieve this, graphical tools for creating, removing, modifying data in database are needed. Parameter estimation tools and MoDeL syntax checking tools are also wanted. We are planning to have this kit in our future version, which will greatly reduce the difficulties for users to construct their own databases.

We believe the future of iGaME is bright !