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Team:DTU Denmark/USERprograminstructions
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<p align="justify">We have put a lot of thought and consideration into which user-definable parameters to include. In the end, we decided that a user-friendly input was the best solution for the beta version of PHUSER. Further down the line, the program can be customized for high-end users, and advanced options made available upon request. For now we keep it simple, and ask only for three main inputs:</p><br> | <p align="justify">We have put a lot of thought and consideration into which user-definable parameters to include. In the end, we decided that a user-friendly input was the best solution for the beta version of PHUSER. Further down the line, the program can be customized for high-end users, and advanced options made available upon request. For now we keep it simple, and ask only for three main inputs:</p><br> | ||
| - | <b>1.</b>Name of biobrick (essentially you can call it whatever you wish), and;<br> | + | <b>1. </b>Name of biobrick (essentially you can call it whatever you wish), and;<br> |
| - | <b>2.</b>Sequence of biobrick (pasted as single-stranded DNA from 5' to 3'). <i>NOTE: Only A's, T's, G's, and C's are accepted as input, i.e. no FASTA-headers or spaces (line shifts are ok).</i><br> | + | <b>2. </b>Sequence of biobrick (pasted as single-stranded DNA from 5' to 3'). <i>NOTE: Only A's, T's, G's, and C's are accepted as input, i.e. no FASTA-headers or spaces (line shifts are ok).</i><br> |
| - | <b>3.</b>Your choice of USER cassette. For now only one is available, but more will follow shortly.<br><br> | + | <b>3. </b>Your choice of USER cassette. For now only one is available, but more will follow shortly.<br><br> |
<p align="justify">As a default in the interface, only two biobrick-submission boxes are available to begin with. If you wish to fuse more than two biobricks in the same reaction, simply click "add another biobrick" and another submission box will appear. The maximum capacity is nine biobricks (may be subject to change).</p><br> | <p align="justify">As a default in the interface, only two biobrick-submission boxes are available to begin with. If you wish to fuse more than two biobricks in the same reaction, simply click "add another biobrick" and another submission box will appear. The maximum capacity is nine biobricks (may be subject to change).</p><br> | ||
Revision as of 21:33, 20 October 2009
| Home | The Team | The Project | Parts submitted | Modelling | Notebook |
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The redoxilator - Genetic design - Applications and perspectives - Results - Safety considerations The USER assembly standard - USER fusion of biobricks USER fusion primer design software - Abstract - Instructions - Output format |
The project The USER fusion primer design software: PHUSER (Primer Help for USER) PHUSER user manual We have put a lot of thought and consideration into which user-definable parameters to include. In the end, we decided that a user-friendly input was the best solution for the beta version of PHUSER. Further down the line, the program can be customized for high-end users, and advanced options made available upon request. For now we keep it simple, and ask only for three main inputs: 1. Name of biobrick (essentially you can call it whatever you wish), and; 2. Sequence of biobrick (pasted as single-stranded DNA from 5' to 3'). NOTE: Only A's, T's, G's, and C's are accepted as input, i.e. no FASTA-headers or spaces (line shifts are ok). 3. Your choice of USER cassette. For now only one is available, but more will follow shortly. As a default in the interface, only two biobrick-submission boxes are available to begin with. If you wish to fuse more than two biobricks in the same reaction, simply click "add another biobrick" and another submission box will appear. The maximum capacity is nine biobricks (may be subject to change). Design your primers with PHUSER here |
Synthetic Biology “Synthetic Biology is an art of engineering new biological systems that don’t exist in nature.” -Paras Chopra & Akhil Kamma In nature, biological molecules work together in complex systems to serve purposes of the cell. In synthetic biology these molecules are used as individual functional units that are combined to form tailored systems exhibiting complex dynamical behaviour. From ‘design specifications’ generated from computational modelling, engineering-based approaches enables the construction of such new specified gene-regulatory networks. The ultimate goal of synthetic biology is to construct systems that gain new functions, and the perspectives of the technology are enormous. It has already been used in several medical projects2 and is predicted to play a major role in biotech-production and environmental aspects. |
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