Difference between revisions of "Team:EPFL/Software"

(first draft software)
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                         <img src="img/computer_to_cell_multi_both.png" style="width: 100%;" />
 
                         <img src="img/computer_to_cell_multi_both.png" style="width: 100%;" />
 
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                         <h2 class="lead animate-box">Build your bioware? is simple</h2>
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                         <h2 class="lead animate-box">Build your own bioware? It's simple</h2>
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                         <p class="sub-lead animate-box">Engineer your cells with biological circuits is incredible, but also very difficult. Intelligene is part of a collection of utilities that allow you to do it quickly and easily.</p>
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                         <p class="sub-lead animate-box">Engineering your cells with new biological circuits  
 +
                            can give them incredible capacities, but can also be a painstaking endeavor.
 +
                            Intelligene is suite of tools meant to fix just that.</p>
 
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                             Synthetic genetic networks are being used more and more frequently in synthetic biology due to their ability to give cells powerful new capabilities while using many of the techniques already common to cell cloning, such as assembly strategies and transformation. Designing the biological organization these circuits, which are often built into plasmid vectors, can be a real challenge. <b>Cello</b>, published in Nature on March 31st, 2016, is a program which allows users to combine data of the desired circuit and data about the host system to generate plasmids containing the fully functional circuits. Over the summer, <b>we developed a suite of software tools meant to increase the user-friendliness, open-source nature, and power of Cello</b>. This required modifying Cello in multiple ways. Firstly, we added an intuitive user interface to Cello to design circuits, eliminating the need for users to understand how to code in Verilog. Secondly, we made Cello accept external inputs, so it could download biological parts from a database. Thirdly, we created and published this database, complete with a variety of features to allow users to interact with the database. Past wiki freeze, we plan to continue working on integration of the database with Cello to allow the seamless transfer of information, and the correct interpretation of the available data.  
+
                             Synthetic genetic networks are being used more and more frequently in synthetic  
 +
                            biology due to their ability to give cells powerful new capabilities while using  
 +
                            many of the techniques already common to cell cloning, such as assembly strategies
 +
                            and transformation. Designing the biological organization these circuits, which  
 +
                            are often built into plasmid vectors, can be a real challenge. <b>Cello</b>,  
 +
                            published in Science on April 1<sup>st</sup>, 2016, is a program which allows users to  
 +
                            combine data of the desired circuit and data about the host system to generate plasmids
 +
                            containing the fully functional circuits. Over the summer, <b>we developed a suite of  
 +
                            software tools meant to increase the user-friendliness, open-source nature, and  
 +
                            power of Cello</b>. This required modifying Cello in multiple ways. Firstly, we  
 +
                            added an intuitive user interface to Cello to design circuits, eliminating the  
 +
                            need for users to understand how to code in Verilog. Secondly, we made Cello  
 +
                            accept external inputs, so it could download biological parts from a database.  
 +
                            Thirdly, we created and published this database, complete with a variety of  
 +
                            features to allow users to interact with the database. Past wiki freeze, we  
 +
                            plan to continue working on integration of the database with Cello to allow  
 +
                            the seamless transfer of information, and the correct interpretation of the  
 +
                            available data.  
 
                         </p>
 
                         </p>
 
                     </div>
 
                     </div>
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                 <div class="container">
 
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                        <span class="sopra-lead">oh</span>
 
 
                         <h2 class="lead">Cello</h2>
 
                         <h2 class="lead">Cello</h2>
 
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                                 <h3>User interface</h3>
 
                                 <h3>User interface</h3>
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                                 <p>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </p>
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                                 <p>Improves user experience and eliminates the need to understand Verilog Code</p>
 
                             </div>
 
                             </div>
 
                         </div>
 
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                             <div class="text">
 
                                 <h3>Scaffold compatibility</h3>
 
                                 <h3>Scaffold compatibility</h3>
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                                 <p>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </p>
+
                                 <p>Modified to work with dCas9-based biochemistries, and handle repeated parts correctly.</p>
 
                             </div>
 
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                                 <h3>Database</h3>
 
                                 <h3>Database</h3>
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                                 <p>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </p>
+
                                 <p>Improved transfer of information by accepting information from database passed in JSON format.</p>
 
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                             <a href="#" class="btn btn-primary btn-cta">learn more</a>
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                             <a href="https://2016.igem.org/Team:EPFL/software_cello" class="btn btn-primary btn-cta">learn more</a>
 
                         </div>
 
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                                 <h3>Parts</h3>
 
                                 <h3>Parts</h3>
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                                 <p>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </p>
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                                 <p>Modifiable databases of parts allow gates to be built using custom parts.</p>
 
                             </div>
 
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                             <div class="text">
 
                                 <h3>User Interface</h3>
 
                                 <h3>User Interface</h3>
−
                                 <p>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </p>
+
                                 <p>Intuitive and easy to use, the User Interface relies on beautiful forms and simple dragging-and-dropping features.</p>
 
                             </div>
 
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                                 <h3>API</h3>
 
                                 <h3>API</h3>
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                                 <p>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </p>
+
                                 <p>Comes with an API so that it can be called from external programs, such as Cello.</p>
 
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                             </div>
 
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                         <div class="btn-action">
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                             <a href="#" class="btn btn-primary btn-cta">Learn more</a>
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                             <a href="https://2016.igem.org/Team:EPFL/software_database" class="btn btn-primary btn-cta">Learn more</a>
 
                         </div>
 
                         </div>
 
                     </div>
 
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Revision as of 22:14, 19 October 2016

iGEM EPFL 2016

Build your own bioware? It's simple

Engineering your cells with new biological circuits can give them incredible capacities, but can also be a painstaking endeavor. Intelligene is suite of tools meant to fix just that.

Synthetic genetic networks are being used more and more frequently in synthetic biology due to their ability to give cells powerful new capabilities while using many of the techniques already common to cell cloning, such as assembly strategies and transformation. Designing the biological organization these circuits, which are often built into plasmid vectors, can be a real challenge. Cello, published in Science on April 1st, 2016, is a program which allows users to combine data of the desired circuit and data about the host system to generate plasmids containing the fully functional circuits. Over the summer, we developed a suite of software tools meant to increase the user-friendliness, open-source nature, and power of Cello. This required modifying Cello in multiple ways. Firstly, we added an intuitive user interface to Cello to design circuits, eliminating the need for users to understand how to code in Verilog. Secondly, we made Cello accept external inputs, so it could download biological parts from a database. Thirdly, we created and published this database, complete with a variety of features to allow users to interact with the database. Past wiki freeze, we plan to continue working on integration of the database with Cello to allow the seamless transfer of information, and the correct interpretation of the available data.

Cello

User interface

Improves user experience and eliminates the need to understand Verilog Code

Scaffold compatibility

Modified to work with dCas9-based biochemistries, and handle repeated parts correctly.

Database

Improved transfer of information by accepting information from database passed in JSON format.

learn more
intelligene.plus

Database

Parts

Modifiable databases of parts allow gates to be built using custom parts.

User Interface

Intuitive and easy to use, the User Interface relies on beautiful forms and simple dragging-and-dropping features.

API

Comes with an API so that it can be called from external programs, such as Cello.

Learn more