Différences entre les versions de « CAD Tools for Synthetic Biology »
| Ligne 1 : | Ligne 1 : | ||
= Presentation = | = Presentation = | ||
| − | The | + | The evolution of microelectronics has been possible through the improvement of the technology, but also thanks to the creation, in parallel, of dedicated Computer-Aided Design (CAD) tools, namely Electronic Design Automation (EDA). The development of the same kind of software in the domain of synthetic biology, a Genetic Design Automation (GDA) tool, would be necessary to support the expansion of this new engineering domain. The aim of our work is to give the outlines of such a GDA by adapting tools and methods that have already proven themselves in the field of microelectronics. The global project is illustrated in the following figure. |
[[Fichier:EDA.png|centré|Scheme of the global project of a GDA tool for synthetic biology, based on electronic languages.]] | [[Fichier:EDA.png|centré|Scheme of the global project of a GDA tool for synthetic biology, based on electronic languages.]] | ||
| Ligne 7 : | Ligne 7 : | ||
The first step to achieve this GDA was to design an automatic models generator to create models of biosystems in hardware description languages (HDLs) commonly used in microelectronics (like VHDL-AMS). The development of this tool began as part of the iGEM 2011 and was carried out by the ENSPS-STRASBOURG team.<br /> | The first step to achieve this GDA was to design an automatic models generator to create models of biosystems in hardware description languages (HDLs) commonly used in microelectronics (like VHDL-AMS). The development of this tool began as part of the iGEM 2011 and was carried out by the ENSPS-STRASBOURG team.<br /> | ||
| − | In the following sections, you will find a video tutorial to | + | In the following sections, you will find a video tutorial to gain knowledge of the handling of the software, the latest version of the software for download, as well as three examples of biosystems modeled using this software. |
= Tutorial = | = Tutorial = | ||
| − | A video tutorial of the automated model generator which was | + | A video tutorial of the automated model generator which was recorded for iGEM 2011 is available on [http://www.youtube.com/watch?v=X74PHfemkz4 Youtube]. Only minor graphical modifications of the interface were done since this video. |
= Downloads = | = Downloads = | ||
| Ligne 16 : | Ligne 16 : | ||
== Automated model generator == | == Automated model generator == | ||
| − | You can download the software | + | You can download the software here :[[:File:Model_Generatorv0.1.zip]].<br /> |
Compatibility : Windows XP or superior.<br /> | Compatibility : Windows XP or superior.<br /> | ||
After entering the system, this software generates different models files. However, to simulate the system, [http://www.dolphin.fr/medal/products/smash/smash_overview.php Dolphin SMASH] is requiered. | After entering the system, this software generates different models files. However, to simulate the system, [http://www.dolphin.fr/medal/products/smash/smash_overview.php Dolphin SMASH] is requiered. | ||
| Ligne 24 : | Ligne 24 : | ||
=== microRNAs detector === | === microRNAs detector === | ||
| − | The model files for the biosystem from Xie ''et al.'' can be | + | The model files for the biosystem from Xie ''et al.'' can be downloaded here: [[:File:miR Detector.zip]] |
Reference: ''Z. Xie, L. Wroblewska, L. Prochazka, R. Weiss, and Y. Benenson, “Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells,” Science, vol. 333, pp. 1307-1311, 2011.'' | Reference: ''Z. Xie, L. Wroblewska, L. Prochazka, R. Weiss, and Y. Benenson, “Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells,” Science, vol. 333, pp. 1307-1311, 2011.'' | ||
| Ligne 30 : | Ligne 30 : | ||
=== Biological half-adder === | === Biological half-adder === | ||
| − | The model files for the biosystem from Ausländer ''et al.'' can be | + | The model files for the biosystem from Ausländer ''et al.'' can be downloaded here: [[:File:Half-adder.zip]] |
Reference: ''S. Ausländer, D. Ausländer, M. Müller, M. Wieland, and M. Fussenegger, “Programmable single-cell mammalian biocomputers.,” Nature, vol. 487, no. 7405, pp. 123–7, Jul. 2012.'' | Reference: ''S. Ausländer, D. Ausländer, M. Müller, M. Wieland, and M. Fussenegger, “Programmable single-cell mammalian biocomputers.,” Nature, vol. 487, no. 7405, pp. 123–7, Jul. 2012.'' | ||
| Ligne 36 : | Ligne 36 : | ||
=== Biological oscillator === | === Biological oscillator === | ||
| − | The model files for the biosystem from Stricker ''et al.'' can be | + | The model files for the biosystem from Stricker ''et al.'' can be downloaded here: [[:File:Oscillator.zip]] |
Reference: ''J. Stricker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring, and J. Hasty, “A fast, robust and tunable synthetic gene oscillator.,” Nature, vol. 456, no. 7221, pp. 516–9, Nov. 2008.'' | Reference: ''J. Stricker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring, and J. Hasty, “A fast, robust and tunable synthetic gene oscillator.,” Nature, vol. 456, no. 7221, pp. 516–9, Nov. 2008.'' | ||
Version actuelle datée du 22 novembre 2013 à 22:41
Presentation
The evolution of microelectronics has been possible through the improvement of the technology, but also thanks to the creation, in parallel, of dedicated Computer-Aided Design (CAD) tools, namely Electronic Design Automation (EDA). The development of the same kind of software in the domain of synthetic biology, a Genetic Design Automation (GDA) tool, would be necessary to support the expansion of this new engineering domain. The aim of our work is to give the outlines of such a GDA by adapting tools and methods that have already proven themselves in the field of microelectronics. The global project is illustrated in the following figure.
The first step to achieve this GDA was to design an automatic models generator to create models of biosystems in hardware description languages (HDLs) commonly used in microelectronics (like VHDL-AMS). The development of this tool began as part of the iGEM 2011 and was carried out by the ENSPS-STRASBOURG team.
In the following sections, you will find a video tutorial to gain knowledge of the handling of the software, the latest version of the software for download, as well as three examples of biosystems modeled using this software.
Tutorial
A video tutorial of the automated model generator which was recorded for iGEM 2011 is available on Youtube. Only minor graphical modifications of the interface were done since this video.
Downloads
Automated model generator
You can download the software here :File:Model_Generatorv0.1.zip.
Compatibility : Windows XP or superior.
After entering the system, this software generates different models files. However, to simulate the system, Dolphin SMASH is requiered.
Models files of three biosystems
microRNAs detector
The model files for the biosystem from Xie et al. can be downloaded here: File:miR Detector.zip
Reference: Z. Xie, L. Wroblewska, L. Prochazka, R. Weiss, and Y. Benenson, “Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells,” Science, vol. 333, pp. 1307-1311, 2011.
Biological half-adder
The model files for the biosystem from Ausländer et al. can be downloaded here: File:Half-adder.zip
Reference: S. Ausländer, D. Ausländer, M. Müller, M. Wieland, and M. Fussenegger, “Programmable single-cell mammalian biocomputers.,” Nature, vol. 487, no. 7405, pp. 123–7, Jul. 2012.
Biological oscillator
The model files for the biosystem from Stricker et al. can be downloaded here: File:Oscillator.zip
Reference: J. Stricker, S. Cookson, M. R. Bennett, W. H. Mather, L. S. Tsimring, and J. Hasty, “A fast, robust and tunable synthetic gene oscillator.,” Nature, vol. 456, no. 7221, pp. 516–9, Nov. 2008.