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.  
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==ACHIEVEMENTS==
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We have proved that electronics and biology can be combined and work together if the synthetic biology field evolve towards more complex model designing. Our software is currently able to simulate the more complex biosystems published, thanks to the powerfulness of electronic tools. But now, we have to extend the concept, and build a new version of the software, more “biologists-friendly”, and more efficient.
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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>
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The work we have realized this year is just a part of the software suite, as you can see below :
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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>
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==NEXT VERSION==
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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>
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For our team, the next step will consist of developing this software in two ways.  
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The first way consists of improving the software, so as to be as close as possible to the biologists’ needs. Indeed, several things need to be done:<br>
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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>
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1- PARTNERSHIPS WITH BIOLOGISTS: This will go along with partnerships with one or more teams in 2012 to have a better interaction between what we want to and what the biologists really needs. This year is a test for us, and we are open to any suggestion to improve our software.<br>
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2- COLLABORATION WITH OTHER SOFTWARE TEAMS: We have a lot of things to learn about other teams, because some teams are close to have realized some functions we want to add in our software suite.<br><br>
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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>
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The second way is to add several functions to our software, and integrate step by step the missing elements of the suite.<br>
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1- USER INTERFACE : to integrate a drag&drop interface so as to build the block diagram of the system will be a new functionality of the future software.<br>
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In parallel, we are thinking of a completely new version, which will use another languages 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.
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2- COMMUNICATION: Integrate a communication between both models. In the future version, one description will be done for both models, thanks to the graphical user interface.<br>
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3- SIMULATION: The next version will integrate new simulation parameters, so as to increase the possibilities of the system.<br>
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Revision as of 18:31, 27 October 2011

Future plans

ACHIEVEMENTS

We have proved that electronics and biology can be combined and work together if the synthetic biology field evolve towards more complex model designing. Our software is currently able to simulate the more complex biosystems published, thanks to the powerfulness of electronic tools. But now, we have to extend the concept, and build a new version of the software, more “biologists-friendly”, and more efficient. The work we have realized this year is just a part of the software suite, as you can see below :


NEXT VERSION

For our team, the next step will consist of developing this software in two ways. The first way consists of improving the software, so as to be as close as possible to the biologists’ needs. Indeed, several things need to be done:
1- PARTNERSHIPS WITH BIOLOGISTS: This will go along with partnerships with one or more teams in 2012 to have a better interaction between what we want to and what the biologists really needs. This year is a test for us, and we are open to any suggestion to improve our software.
2- COLLABORATION WITH OTHER SOFTWARE TEAMS: We have a lot of things to learn about other teams, because some teams are close to have realized some functions we want to add in our software suite.

The second way is to add several functions to our software, and integrate step by step the missing elements of the suite.
1- USER INTERFACE : to integrate a drag&drop interface so as to build the block diagram of the system will be a new functionality of the future software.
2- COMMUNICATION: Integrate a communication between both models. In the future version, one description will be done for both models, thanks to the graphical user interface.
3- SIMULATION: The next version will integrate new simulation parameters, so as to increase the possibilities of the system.

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