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From 2011.igem.org

CHOICE OF THE TOOLS

The first step was to choose a programming language suitable for making our implementation. Ideally, we wanted to use the same language to program both GUI and file generation. In a previous project, we have already programed a GUI, in C++ language, with the framework QT creator. Moreover, the C++ is a powerful multi-purpose language which could be suitable for making our file generation. Another advantage of C++ is that we have a C/C++ programming module in our course, and we thought that it was probably better to implement this program with a language we already knew. We have so decided to use C++, for its versatility, and because we are quite used to it.

Qt creator – presentation

Then, we need to find an electronic circuit simulator which enables us to simulate the systems as electronic systems. For that, we choose SMASH (Dolphin), because this software is one of the most accomplished simulation software, so as to simulate both digital and analog electronics. SMASH - presentation

VERSION 1 - « Behavioral Code Generator  »

Introduction

The first step of the project was to validate the concept of the program. We have so decided to build a first version of the software, with simple digital models. This version, entitled “Behavioral Code Generator”, enables the user to simulate a logic version of the mechanisms and reactions.

Approach

The aim of this first implementation is to validate the idea of building a software which generates automatically models for each reaction of a system. Those models are electrical models of two basic biological mechanisms, written in VHDL for the first time, as seen in the[Models LIEN VERS MODELES VHDL] section. After that, this generation can be simulated directly with an electronic circuit simulator, as a digital electronic circuit.

File generation

The goal is to generate automatically VHDL files which are representative of the different reactions of the system. For that, our approach is to use pattern files, and to fill up those files with the right variables (species, names…), depending on the reactions implemented by the user.

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 a VHDL-AMS modelisation.

For the moment our software asks the user to specify all the species characteristics manually. However there are many databases which already gathered that information like the [http://partsregistry.org/Main_Pagewebsite http://partsregistry.org/Main_Pagewebsite] . Then we could imagine a program’s module that would get all the available protein, suggests them to the biologist and downloads all the needed characteristics.

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.

In the same idea, we could imagine than the software can launch the VHDL simulator (DOLPHIN Smash Vision) directly, with just a button pressed by the user. Then, the system generated could be simulated automatically.

Concerning the simulation, currently only basic stimuli are available. We could imagine extending the available simulation features for the system.