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Team:ENSPS-Strasbourg/Future
From 2011.igem.org
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The current work has validated a crucial part of our works, to prove that synthetic biology and digital microelectronics could be correlated, and this part of electronics could be useful for helping biologists to create bio-systems. The current software version enables to create a system with two basic biological mechanisms simulated thanks to VHDL or VHDL-AMS models. Two simulations are available, one behavioral, and the other conservative. | The current work has validated a crucial part of our works, to prove that synthetic biology and digital microelectronics could be correlated, and this part of electronics could be useful for helping biologists to create bio-systems. The current software version enables to create a system with two basic biological mechanisms simulated thanks to VHDL or VHDL-AMS models. Two simulations are available, one behavioral, and the other conservative. | ||
| - | For the moment our software asks the user to specify all the species characteristics manually. However, the iGEM database (http://partsregistry.org/Main_Pagewebsite) already gathered that information. Then, a future program’s module will be created so as to get all the available proteins, suggests them to the biologist and downloads all the needed characteristics. In this way, the work of another Europe software team, ANKARA, could be complementary to our work. Indeed, the software would pick up the different proteins and structure, then the biologist select them and build his system, and simulate it into the electrical circuit simulator. | + | <br> |
| - | A first improvement will be to interconnect both versions of the program. The idea is to build a system and simulated it both by behavioral and conservative models. The idea behind that is to first simulate a behavioral version of the system to have a global idea of the behavior, and then to go to a conservative version, just by changing the initial values of the species. | + | For the moment our software asks the user to specify all the species characteristics manually. However, the iGEM database (http://partsregistry.org/Main_Pagewebsite) already gathered that information. Then, a future program’s module will be created so as to get all the available proteins, suggests them to the biologist and downloads all the needed characteristics. In this way, the work of another Europe software team, ANKARA, could be complementary to our work. Indeed, the software would pick up the different proteins and structure, then the biologist select them and build his system, and simulate it into the electrical circuit simulator.<br> |
| - | Furthermore, the current interface is not as user friendly as we want it to be. A decent drag and drop system would be required, so as to enable the user to easily add new species, blocks and new reactions of his system. Then, the interaction between different blocks would be more visual, and the user could have in real time an overview of the whole system. | + | <br> |
| - | Concerning the simulation, currently only basic stimuli are available. We will also extend the available simulation parameters for the system, especially for AMS models. | + | A first improvement will be to interconnect both versions of the program. The idea is to build a system and simulated it both by behavioral and conservative models. The idea behind that is to first simulate a behavioral version of the system to have a global idea of the behavior, and then to go to a conservative version, just by changing the initial values of the species.<br> |
| - | In the same idea, we could imagine than the software can launch the VHDL simulator directly, with just a button pressed by the user. For instance, each different simulator needs specific file. In a first time, because we use SMASH, the simulation software could be directly lauched by our application. Then, the system generated could be simulated automatically. | + | <br> |
| + | Furthermore, the current interface is not as user friendly as we want it to be. A decent drag and drop system would be required, so as to enable the user to easily add new species, blocks and new reactions of his system. Then, the interaction between different blocks would be more visual, and the user could have in real time an overview of the whole system. <br> | ||
| + | <br> | ||
| + | Concerning the simulation, currently only basic stimuli are available. We will also extend the available simulation parameters for the system, especially for AMS models. <br> | ||
| + | <br> | ||
| + | In the same idea, we could imagine than the software can launch the VHDL simulator directly, with just a button pressed by the user. For instance, each different simulator needs specific file. In a first time, because we use SMASH, the simulation software could be directly lauched by our application. Then, the system generated could be simulated automatically. <br> | ||
| + | <br> | ||
In parallel, we are thinking of a completely new version, which will use another languages widely used in microelectronics called SystemC and SystemC-AMS. Those two languages are quite recent, and they are currently under development. The idea of SystemC and SystemC-AMS is to be close to VHDL and VHDL-AMS, but based on C++, and totally open source. Our approach will be to develop models in those languages, and use the C++ to totally integrate the GUI, the file Generation and the simulation into the same software. | In parallel, we are thinking of a completely new version, which will use another languages widely used in microelectronics called SystemC and SystemC-AMS. Those two languages are quite recent, and they are currently under development. The idea of SystemC and SystemC-AMS is to be close to VHDL and VHDL-AMS, but based on C++, and totally open source. Our approach will be to develop models in those languages, and use the C++ to totally integrate the GUI, the file Generation and the simulation into the same software. | ||
Revision as of 13:13, 21 September 2011
Further Improvements
The current work has validated a crucial part of our works, to prove that synthetic biology and digital microelectronics could be correlated, and this part of electronics could be useful for helping biologists to create bio-systems. The current software version enables to create a system with two basic biological mechanisms simulated thanks to VHDL or VHDL-AMS models. Two simulations are available, one behavioral, and the other conservative.
For the moment our software asks the user to specify all the species characteristics manually. However, the iGEM database (http://partsregistry.org/Main_Pagewebsite) already gathered that information. Then, a future program’s module will be created so as to get all the available proteins, suggests them to the biologist and downloads all the needed characteristics. In this way, the work of another Europe software team, ANKARA, could be complementary to our work. Indeed, the software would pick up the different proteins and structure, then the biologist select them and build his system, and simulate it into the electrical circuit simulator.
A first improvement will be to interconnect both versions of the program. The idea is to build a system and simulated it both by behavioral and conservative models. The idea behind that is to first simulate a behavioral version of the system to have a global idea of the behavior, and then to go to a conservative version, just by changing the initial values of the species.
Furthermore, the current interface is not as user friendly as we want it to be. A decent drag and drop system would be required, so as to enable the user to easily add new species, blocks and new reactions of his system. Then, the interaction between different blocks would be more visual, and the user could have in real time an overview of the whole system.
Concerning the simulation, currently only basic stimuli are available. We will also extend the available simulation parameters for the system, especially for AMS models.
In the same idea, we could imagine than the software can launch the VHDL simulator directly, with just a button pressed by the user. For instance, each different simulator needs specific file. In a first time, because we use SMASH, the simulation software could be directly lauched by our application. Then, the system generated could be simulated automatically.
In parallel, we are thinking of a completely new version, which will use another languages widely used in microelectronics called SystemC and SystemC-AMS. Those two languages are quite recent, and they are currently under development. The idea of SystemC and SystemC-AMS is to be close to VHDL and VHDL-AMS, but based on C++, and totally open source. Our approach will be to develop models in those languages, and use the C++ to totally integrate the GUI, the file Generation and the simulation into the same software.
