Team:Amsterdam/software/designer/setup

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<h1>Plasmid Design Tool: The Setup</h1>
 
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We have designed an online tool where a user can create their Cellular Logbook in silico by giving a backbone sequence and selecting one or more sensors manually or predefined from the parts registry database.An algorithm then computes one or more plasmids, taking into account the rules we use for our real life Cellular Logbook, and outputs the appropriategenbank files as well as the visualized version of the plasmid. The tool will also generate all possible permutations of gel bands which can be used as a read-out sheet for the gel electrophoresis results. By using this tool we are able to quickly design a plasmid with multiple sensors.
 
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<h2>The Plasmid Design Algorithm</h2>
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When designing the plasmid, the tool takes the following rules into account:
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<h1>Cellular Logbook Construct Designer: Setup</h1>
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We have designed an online tool where a user can create their Cellular Logbook in silico by giving a backbone sequence and selecting one or more sensors manually or predefined from the parts registry database. An algorithm then computes one or more plasmids, taking into account the rules we use for our real life Cellular Logbook, and outputs the appropriate genbank files as well as the visualized version of the plasmid. The tool will also generate all possible permutations of gel bands which can be used as a read-out sheet for the gel electrophoresis results. By using this tool we are able to quickly design a plasmid with multiple sensors.
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*Each given sensor generates the following sequences on the memory plasmid: sensor, ribosomal binding site, zinc finger, linker, myc tag, methyltransferase and terminator.
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*Each given sensor generates the following sequences on the restriction plasmid: zinc finger recognition site, 120bp random dna, methyltransferase recognition site, 120bp random dna and again the zinc finger recognition site.
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*Each zinc finger is unique and taken from the 'ZifBase' [http://web.iitd.ac.in/~sundar/zifbase/] database.
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<h2>Genbank Output</h2>
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[[File:Amsterdam_tool_genbank.png|right|300px]]
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Standard formats for biological data are essential to communicate and pass along biological findings. The Genbank format is the most widely used format for genome and sequence annotation. As such the Plasmid Designer is able to produce Genbank files for each plasmid with the click of a button. This way the user can use the designed construct in other biological tools such as the freeware plasmid editor ApE[http://biologylabs.utah.edu/jorgensen/wayned/ape/].
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<h2>Plasmid Visualization</h2>
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[[File:Amsterdam tool visualization1.png|left|300px]]
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In order to grant the user a quick and dynamic overview of the plasmids that were just designed, a visualization of each plasmid is available with just a click on a button. Each of these visualized plasmids shows the specific features of that plasmid by color code. Hovering over each feature gives additional information, and clicking on a feature gives its DNA sequence.
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*The ribosomal binding site, linker, myc-tag, methyltransferase and terminator are randomly chosen from a pre-made list available to the tool.
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*Forbidden sequences are given both absolute and dynamicly, and sequences newly generated on the plasmid can not contain any of these forbidden sequences.
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<h2>Gel Readout</h2>
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[[File:Amsterdam_tool_readout.png|right|300px]]
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The amount of gel bands increases exponentially as more sensors are engineered into the construct. Therefore having to figure out which signals have come to expression and which have not can prove to be an impossible task. We have included an algorithm inside the tool that computes all possible band combinations, and selects the bands that belong to each band position given by the user.
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*Only 5 sensors can be engineered into one memory plasmid. If more sensors are engineered on one plasmid, the size of the plasmid will grow too big.
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Input: Sensors and Backbone
 
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There are two mandatory inputs: Sensors and the backbone
 
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Pre-defined sensors are taken from the Parts Registry database. These are given using hidden forms, generated by a Python script due to Javascript limitations. The user can also submit manual sensors in fasta or genbank format, or a combination of pre-defined and manual sensors.
 
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The backbone is given manually in fasta or genbank format.
 
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<h2>Genbank Files</h2>
 
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Each plasmid can be given in a Genbank file. Due to Javascript limitations and the fact that we do not have access to storing files temporarily on the iGEM server by means of scripting.
 
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<h2>Plasmid Visualization</h2>
 
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Each plasmid can be generated visually to give a quick overview of its contents. The visualization shows the plasmid containing each feature. The features have a different color, depending on the type of feature. By hovering over the feature with the mouse button, the full description of the feature is displayed, along with the feature type and its length. Clicking on a feature will generate the DNA sequence of that feature.
 
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<h2>Read out</h2>
 
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For each detectable signal engineered in the Cellular Logbook, the amount of band combinations gets exponentially higher. When trying to maximizing the Cellular Logbook by having a high amount of sensors, interpreting a gel becomes an almost impossible task.
 
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The tool therefore provides an algorithm that is able to compute which bands belong to which sensors, and as such which sensors have been present in the Cellular Logbook. This read out algorithm works by taking the user input, which consists of a position on the gel for each band, and generating all different possible band sizes for each band. The band size closest to each of the given input sizes is then given as an output, together with the corresponding input signal.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
 
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Latest revision as of 22:23, 16 September 2012