Difference between revisions of "Team:EPFL/Software"

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      <div class="spacer h150"></div>
  
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<div class="simple-page centered-page">
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            <section class="">
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                <div class="container">
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                    <div class="col-md-10 col-md-offset-1 text-center">
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                        <img src="https://static.igem.org/mediawiki/2016/5/52/Computer_to_cell_multi_both.png" style="width: 100%;" />
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                        <div class="spacer h20"></div>
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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">Engineering your cells with new biological circuits
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                            can give them incredible capacities, but can also be a painstaking endeavor.
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                            Intelligene is suite of tools meant to fix just that.</p>
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                        <div class="spacer h20"></div>
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                        <hr class="animate-box"/>
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                        <div class="spacer h20"></div>
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                        <p class="sub-lead justified animate-box">
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                            Synthetic genetic networks are being used more and more frequently in synthetic
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                            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>
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                    </div>
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                </div>
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            </section>
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        </div>
  
  
  
  
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<div class="column full_size">
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        <div class="simple-page">
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.</p>
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            <section class="lightGray features">
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                <div class="container">
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                    <div class="col-md-7">
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                        <h2 class="lead">Cello</h2>
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                        <div class="feature">
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                            <div class="icon">
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                                <i class="fa fa-check"></i>
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                            </div>
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                            <div class="text">
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                                <h3>User interface</h3>
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                                <p>Improves user experience and eliminates the need to understand Verilog Code</p>
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                            </div>
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                        </div>
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                        <div class="feature">
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                            <div class="icon">
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                                <i class="fa fa-check"></i>
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                            </div>
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                            <div class="text">
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                                <h3>Scaffold compatibility</h3>
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                                <p>Modified to work with dCas9-based biochemistries, and handle repeated parts correctly.</p>
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                            </div>
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                        </div>
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                        <div class="feature">
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                            <div class="icon">
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                                <i class="fa fa-check"></i>
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                            </div>
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                            <div class="text">
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                                <h3>Database</h3>
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                                <p>Improved transfer of information by accepting information from database passed in JSON format.</p>
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                            </div>
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                        </div>
  
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                        <div class="btn-action">
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                            <a href="https://2016.igem.org/Team:EPFL/Software_CELLO" class="btn btn-primary btn-cta">learn more</a>
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                        </div>
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                    </div>
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                    <div class="col-md-5">
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                        <div class="spacer h50"></div>
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                        <figure class="feature-image medium animate-box">
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                            <img src="https://static.igem.org/mediawiki/2016/5/5f/Macbook_cello_UI.png" alt="">
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                        </figure>
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                    </div>
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                </div>
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            </section>
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        </div>
  
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<h5> Inspiration </h5>
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        <div class="simple-page">
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<p>
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            <section class="features">
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Here are a few examples from previous teams:
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                <div class="container">
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</p>
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                    <div class="col-md-5 col-md-pull-4">
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<ul>
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                        <div class="spacer h50"></div>
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<li><a href="https://2013.igem.org/Team:TU-Munich/Results/Software">TU Munich 2013</a></li>
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                        <figure class="feature-image medium animate-box">
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">Heidelberg 2014</a></li>
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                            <img src="https://static.igem.org/mediawiki/2016/b/b5/Macbook_intelligene.plus_sequence_tagger.png" alt="">
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<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">Aachen 2014</a></li>
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                        </figure>
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</ul>
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                    </div>
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                    <div class="col-md-7">
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                        <span class="sopra-lead">intelligene.plus</span>
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                        <h2 class="lead">Database</h2>
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                        <div class="feature">
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                            <div class="icon">
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                                <i class="fa fa-check"></i>
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                            </div>
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                            <div class="text">
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                                <h3>Parts</h3>
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                                <p>Modifiable databases of parts allow gates to be built using custom parts.</p>
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                            </div>
 +
                        </div>
 +
                        <div class="feature">
 +
                            <div class="icon">
 +
                                <i class="fa fa-check"></i>
 +
                            </div>
 +
                            <div class="text">
 +
                                <h3>User Interface</h3>
 +
                                <p>Intuitive and easy to use, the User Interface relies on beautiful forms and simple dragging-and-dropping features.</p>
 +
                            </div>
 +
                        </div>
 +
                        <div class="feature">
 +
                            <div class="icon">
 +
                                <i class="fa fa-check"></i>
 +
                            </div>
 +
                            <div class="text">
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                                <h3>API</h3>
 +
                                <p>Comes with an API so that it can be called from external programs, such as Cello.</p>
 +
                            </div>
 +
                        </div>
  
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</div>
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                        <div class="btn-action">
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                            <a href="https://2016.igem.org/Team:EPFL/Software_DATABASE" class="btn btn-primary btn-cta">Learn more</a>
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                        </div>
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                    </div>
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                </div>
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            </section>
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        </div>
  
 
</html>
 
</html>
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{{RISE_foot}}

Latest revision as of 03:06, 20 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