Difference between revisions of "Team:EPFL/Software"

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                    <div class="col-md-10 col-md-offset-1 text-center">
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                        <img src="img/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 bioware? is 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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                            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.
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            </section>
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        </div>
  
  
  
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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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                        <span class="sopra-lead">oh</span>
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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>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </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>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </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>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </p>
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                            </div>
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                        </div>
  
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<h5> Inspiration </h5>
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                        <div class="btn-action">
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<p>
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                            <a href="#" class="btn btn-primary btn-cta">learn more</a>
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Here are a few examples from previous teams:
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</p>
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                    </div>
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<ul>
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                    <div class="col-md-5">
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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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                        <div class="spacer h50"></div>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Software">Heidelberg 2014</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:Aachen/Project/Measurement_Device#Software">Aachen 2014</a></li>
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                            <img src="img/macbook_cello_UI.png" alt="">
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</ul>
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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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        <div class="simple-page">
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            <section class="features">
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                <div class="container">
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                    <div class="col-md-5 col-md-pull-4">
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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="img/macbook_intelligene.plus_sequence_tagger.png" alt="">
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                        </figure>
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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>Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts. </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">
 +
                                <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>
 +
                            </div>
 +
                        </div>
 +
                        <div class="feature">
 +
                            <div class="icon">
 +
                                <i class="fa fa-check"></i>
 +
                            </div>
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                            <div class="text">
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                                <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>
 +
                            </div>
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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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                        </div>
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                    </div>
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                </div>
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            </section>
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        </div>
  
 
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{{RISE_foot}}

Revision as of 12:28, 19 October 2016

iGEM EPFL 2016

Build your bioware? is simple

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.

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 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, 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.

oh

Cello

User interface

Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts.

Scaffold compatibility

Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts.

Database

Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts.

learn more
intelligene.plus

Database

Parts

Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts.

User Interface

Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts.

API

Far far away, behind the word mountains, far from the countries Vokalia and Consonantia, there live the blind texts.

Learn more