Team:SYSU-Software/designer

From 2013.igem.org

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<title>Team:SYSU-Software</title>
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             <span id="cast-intruction-text-header">Introduction</span><br>
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             <span id="cast-intruction-text-header">Regulation network:</span><br>
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             Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
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             Protein is the basic functional unit of all purpose of life. We can programme the mechanism among proteins by constructing regulation network; meanwhile,  
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this is also the step that users initially organize their ideas. In the Regulation network part, users can search all kinds of proteins that relates to synthetic
 +
 
 +
biology and drag them in the blank and then arrange the regulatory relationship. Clicking on Protein A, three icons will show on other proteins (for example, protein
 +
 
 +
B) that can be regulated by A. To click on the up arrow means A stimulate the expression of B (up-regulation) while the down arrow means repression (down-regulation).
 +
 
 +
The chain icon means A and B are programmed to be co-expressed. Different regulatory factors are provided to meet the demand of regulatory method. Users can design
 +
 
 +
their functional network but not gene circuits thus they can focus on the ideas without the bothering of technical questions.
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           <span id="cast-intruction-text">
           <span id="cast-intruction-text">
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             <span id="cast-intruction-text-header">Introduction</span><br>
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             <span id="cast-intruction-text-header">Gene circuit:</span><br>
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            Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
+
          Followed by Regulation network part, CAST will generate default gene circuits automatically. Also, the circuits can be optimized by users according to  
 +
 
 +
special demand of materials or methods. Simultaneously, the simulation of this network will be displayed. The parameters of proteins can be adjusted by dragging the
 +
 
 +
columns, and thus, the model will be real-time adjusted. Furthermore, we can view the model by detail; in the simulation window, users can compare some curves they
 +
 
 +
concentrate, or view the model influenced by stochastic noise or time delay. Inducers’ effects will be also reflected in the model.
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           <span id="cast-intruction-text">
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             <span id="cast-intruction-text-header">Introduction</span><br>
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             <span id="cast-intruction-text-header">Plasmid & protocol:</span><br>
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             Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
+
             Circuit design is not our final goal. Gene circuits designed by our software will be composed into a plasmid automatically. Furthermore, protocol for
 +
 
 +
assembling plasmid is also provided step by step. Beginners are able to accomplish their idea with our direction conveniently. Designed plasmid is presented as a
 +
 
 +
circle and all the sequence is annotated and displayed at the head of the window. Biobricks locate in different loci in plasmid will be marked and all the sequences
 +
 
 +
can be revised by users. Lab protocol for standard Biobricks assembling is presented in our software for amateurs. Following the directions, people with little
 +
 
 +
experience in wet lab will be able to create their own engineered bacterium and feel the magic of synthetic biology.
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           <span id="cast-intruction-text">
           <span id="cast-intruction-text">
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             <span id="cast-intruction-text-header">Introduction</span><br>
+
             <span id="cast-intruction-text-header">Other functions:</span><br>
-
             Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
+
             Aside from the basic functions listed above, there are some auxiliary functions which help a lot.
 +
Introduce Biobrick. In the interface of user account, entering “my files”, people can build and upload their novel biobricks by typing in the sequence and describe the
 +
 
 +
parameters and type. These data can be edited and managed online.
 +
    Output SBOL file. The created biobricks will be compiled into SBOL automatically and thus users can get the file according to the information of the  
 +
 
 +
biobrick.
 +
    File sharing. Not only the biobricks, but also the ideas can be shared by CAST. Users’ result of their ideas: regulation network, plasmid constructed and
 +
 
 +
simulation can be stored on CAST and shared between researchers.
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Revision as of 12:20, 26 September 2013

Team:SYSU-Software new

CAST (Computer Aided Synbio Tool)- An Integrated Tool
for Synthetic Biology
Regulation network:
Protein is the basic functional unit of all purpose of life. We can programme the mechanism among proteins by constructing regulation network; meanwhile, this is also the step that users initially organize their ideas. In the Regulation network part, users can search all kinds of proteins that relates to synthetic biology and drag them in the blank and then arrange the regulatory relationship. Clicking on Protein A, three icons will show on other proteins (for example, protein B) that can be regulated by A. To click on the up arrow means A stimulate the expression of B (up-regulation) while the down arrow means repression (down-regulation). The chain icon means A and B are programmed to be co-expressed. Different regulatory factors are provided to meet the demand of regulatory method. Users can design their functional network but not gene circuits thus they can focus on the ideas without the bothering of technical questions.
Gene circuit:
Followed by Regulation network part, CAST will generate default gene circuits automatically. Also, the circuits can be optimized by users according to special demand of materials or methods. Simultaneously, the simulation of this network will be displayed. The parameters of proteins can be adjusted by dragging the columns, and thus, the model will be real-time adjusted. Furthermore, we can view the model by detail; in the simulation window, users can compare some curves they concentrate, or view the model influenced by stochastic noise or time delay. Inducers’ effects will be also reflected in the model.
Plasmid & protocol:
Circuit design is not our final goal. Gene circuits designed by our software will be composed into a plasmid automatically. Furthermore, protocol for assembling plasmid is also provided step by step. Beginners are able to accomplish their idea with our direction conveniently. Designed plasmid is presented as a circle and all the sequence is annotated and displayed at the head of the window. Biobricks locate in different loci in plasmid will be marked and all the sequences can be revised by users. Lab protocol for standard Biobricks assembling is presented in our software for amateurs. Following the directions, people with little experience in wet lab will be able to create their own engineered bacterium and feel the magic of synthetic biology.
Other functions:
Aside from the basic functions listed above, there are some auxiliary functions which help a lot. Introduce Biobrick. In the interface of user account, entering “my files”, people can build and upload their novel biobricks by typing in the sequence and describe the parameters and type. These data can be edited and managed online. Output SBOL file. The created biobricks will be compiled into SBOL automatically and thus users can get the file according to the information of the biobrick. File sharing. Not only the biobricks, but also the ideas can be shared by CAST. Users’ result of their ideas: regulation network, plasmid constructed and simulation can be stored on CAST and shared between researchers.

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