Team:Vanderbilt Software/Project/darwin

From 2014.igem.org

(Difference between revisions)
 
(7 intermediate revisions not shown)
Line 67: Line 67:
     <div id="right_page" class="page">
     <div id="right_page" class="page">
-
    <img src="https://static.igem.org/mediawiki/2014/f/f9/Editing_single_lines.png" class="page_img" width=487 height=322>
 
     </div>
     </div>
</div>
</div>
Line 74: Line 73:
<div id="right_button" class="button"></div>
<div id="right_button" class="button"></div>
 +
<script type="text/javascript" src="https://2014.igem.org/Team:Vanderbilt/subpagebuilder?action=raw&ctype=text/javascript"></script>
 +
 +
<script>
 +
    var builder = new SubPageBuilder();
 +
    var img1 = builder.createPhoto("https://static.igem.org/mediawiki/2014/f/f9/Editing_single_lines.png", "darwin eliminates extra lines in the output file", 487, 322, "darwin eliminates extra lines in the output file");
 +
    var img2 = builder.createPhoto("https://static.igem.org/mediawiki/2014/5/50/Editing_characters_in_lines.png", "darwin's unique method of parsing ORF", 487, 381, "darwin's unique method of parsing ORF");
 +
    var img3 = builder.createPhoto("https://static.igem.org/mediawiki/2014/b/bc/Pipeline_diagram_concurrency.png", "Representation of darwin‘s block processor increasing processing speed", 487, 381, "Representation of darwin‘s block processor increasing processing speed");
 +
 +
    document.getElementById("right_page").appendChild(img1);
 +
    document.getElementById("right_page").appendChild(img2);
 +
    document.getElementById("right_page").appendChild(img3);
 +
</script>
</body>
</body>
</html>
</html>

Latest revision as of 16:37, 26 January 2015

darwin

Program Description

Version control systems sych as git and svn 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.