Team:Johns Hopkins-Software/theSoftware overview
From 2012.igem.org
(Difference between revisions)
(5 intermediate revisions not shown) | |||
Line 8: | Line 8: | ||
</div> | </div> | ||
<br> | <br> | ||
- | AutoGene is an innovative plasmid design suite meant to streamline the | + | AutoGene is an innovative plasmid design suite meant to streamline the processes of annotating and building sequences. Written in Java and Python and consisting of two modules -- AutoPlasmid and AutoDesign -- it first uses a highly curated database of features to search an imported plasmid, scanning the sequence for both perfect and imperfect alignments, and then generating an interactive visualization of the annotated plasmid. Once a plasmid is annotated, a user is then able to alter its contents, using the AutoGene feature database, the biobrick database, as well as custom components. Still in progress, the design module enables structural optimization by maintaining sets of sequence rules and taking an algorithmic approach to minimizing structural violations. Additionally the program reduces the problems caused by restriction sites during application of designs, and proposes the most suitable enzyme selections through an analysis of standard restriction sites libraries. |
<br><br> | <br><br> | ||
The processes will be run on the cloud as a standard web server gateway interface service to dramatically increasing its speed and accessibility while maintaining the same level of accuracy. As a cloud service, it will run its algorithms in parallel and thus have the ability to perform more computationally intense procedures, such as optimizing codons to increase gene expression, and designing the most efficient oligonucleotide sequences for PCR assembly. | The processes will be run on the cloud as a standard web server gateway interface service to dramatically increasing its speed and accessibility while maintaining the same level of accuracy. As a cloud service, it will run its algorithms in parallel and thus have the ability to perform more computationally intense procedures, such as optimizing codons to increase gene expression, and designing the most efficient oligonucleotide sequences for PCR assembly. | ||
Line 20: | Line 20: | ||
Software Goals | Software Goals | ||
</div> | </div> | ||
- | + | <br> | |
<p>We recognized a need for a comprehensive piece of software that provided the means to achieve an easier Plasmid Design process. Manual annotation is simply too time consuming, tedious, and error-prone. We wanted to create something to fix this noticeable setback of existing synthetic biology software. AutoGene sets a new technological standard by bringing automation to the plasmid design process. That being said, we developed a list of specific goals we wished to achieve. We split these goals into two modules, and decided the first set of goals would be achieved by AutoPlasmid, the second set of goals would be achieved by AutoDesign, and together, we would create AutoGene.</p> | <p>We recognized a need for a comprehensive piece of software that provided the means to achieve an easier Plasmid Design process. Manual annotation is simply too time consuming, tedious, and error-prone. We wanted to create something to fix this noticeable setback of existing synthetic biology software. AutoGene sets a new technological standard by bringing automation to the plasmid design process. That being said, we developed a list of specific goals we wished to achieve. We split these goals into two modules, and decided the first set of goals would be achieved by AutoPlasmid, the second set of goals would be achieved by AutoDesign, and together, we would create AutoGene.</p> | ||
Line 43: | Line 43: | ||
<br><br> | <br><br> | ||
</div> | </div> | ||
- | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> | + | <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br> |
</html> | </html> | ||
{{:Team:Johns_Hopkins-Software/header}} | {{:Team:Johns_Hopkins-Software/header}} |