Difference between revisions of "Team:EPFL/Software"

 
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                         <h2 class="lead animate-box">Build your own bioware? It's simple</h2>
 
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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.

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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