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Team:Vanderbilt Software/Novel Approach
From 2014.igem.org
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| - | + | <p>git, svn, and other version control systems focus on differences between lines. Since most | |
| + | DNA file formats split DNA to fixed-length lines, many lines are changed at once, for | ||
| + | example, when inserting a single new line. darwin does away with that by producing a | ||
| + | formatted file representing each ORF on its own line of text, making each edit only modify a | ||
| + | single line of the output text.</p> | ||
| + | <figure> | ||
| + | <img src="https://static.igem.org/mediawiki/2014/f/f9/Editing_single_lines.png"> | ||
| + | <figcaption>Fig1. - darwin eliminates extra lines in the output file</figcaption> | ||
| + | </figure> | ||
| + | |||
| + | <p>Genes can be very long. To combat this, darwin will sample a section of every newly inserted | ||
| + | ORF and compare it to nearby ORFs; if the new ORF is similar to another ORF, it is counted | ||
| + | as “edited,” and darwin only records the character-by-character changes required to | ||
| + | transform the old ORF into the new ORF.</p> | ||
| + | <figure> | ||
| + | <img src="https://static.igem.org/mediawiki/2014/5/50/Editing_characters_in_lines.png"> | ||
| + | <figcaption>Fig2. - darwin's unique method of parsing ORF</figcaption> | ||
| + | </figure> | ||
| + | |||
| + | <p>Finally, darwin uses concurrency to help speed up the process. File I/O is typically extremely slow, | ||
| + | much slower than processing a file data already in memory. Splitting the processing concurrently helps to open up that speed bottleneck.</p> | ||
| + | <figure> | ||
| + | <img src="https://static.igem.org/mediawiki/2014/b/bc/Pipeline_diagram_concurrency.png"> | ||
| + | <figcaption>Fig3. - Representation of darwin‘s block processor increasing processing speed</figcaption> | ||
| + | </figure> | ||
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Latest revision as of 18:09, 18 January 2015
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git, svn, and other version control systems focus on differences between lines. Since most DNA file formats split DNA to fixed-length lines, many lines are changed at once, for example, when inserting a single new line. darwin does away with that by producing a formatted file representing each ORF on its own line of text, making each edit only modify a single line of the output text. 
Genes can be very long. To combat this, darwin will sample a section of every newly inserted ORF and compare it to nearby ORFs; if the new ORF is similar to another ORF, it is counted as “edited,” and darwin only records the character-by-character changes required to transform the old ORF into the new ORF. 
Finally, darwin uses concurrency to help speed up the process. File I/O is typically extremely slow, much slower than processing a file data already in memory. Splitting the processing concurrently helps to open up that speed bottleneck. 
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