https://wiki.umiacs.umd.edu/cbcb/index.php?action=history&feed=atom&title=Cbcb%3APop-Lab%3ASerge-Report 2026-04-13T01:15:01Z Revision history for this page on the wiki MediaWiki 1.43.7 https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Serge-Report&diff=4550&oldid=prev 2009-02-12T23:50:22Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:50, 12 February 2009</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">= February =</ins></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">February 16th</del>, <del style="font-weight: bold; text-decoration: none;">2009</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;b&gt;February 16th, 2009:&lt;/b&gt;&lt;br&gt;</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* I have been working on the materials for my preliminary exam. My preliminary paper is is available [[Media:PaperList.pdf|here]] and the preliminary paper is [[Media:Paper.pdf|here]].</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* I have also met with Dr. Alan Sussman, a member of my preliminary committee, to discuss parallel option for graph algorithms. He pointed me to several papers on graph and hyper</ins>-<ins style="font-weight: bold; text-decoration: none;">graph partitioning. I had been thinking of doing randomized graph algorithms for speedup but using efficient partitioning, the standard graph algorithms can be distributed while minimizing communication. The other option is to use shared</ins>-<ins style="font-weight: bold; text-decoration: none;">memory machines which are more expensive and less available than distributed memory machines.</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* I also implemented two methods for repeat detection in Bambus 2. </ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">** The first splits the graph into strongly connected components using the SeqAn library. The astat is computed on each connected component separately. The motivation is to subdivide metagenomic samples into their constituent organisms and compute astat only on one organism at a time to avoid inadvertently marking abundant organisms as repeats</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">** The second computes all</ins>-<ins style="font-weight: bold; text-decoration: none;">to</ins>-<ins style="font-weight: bold; text-decoration: none;">all shortest paths and the number of shortest paths each node is on. The nodes that are on a large number of shortest paths (more than 1.5 stdev from mean) are marked as repetitive.</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">** Using the combination of these two approaches Brucella_suis_1330 correctly identifies repeats that were previously causing mis-assembly. I also tried the methods on Acid Mine but SeqAn was crashing. </ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* My next steps are to continue writing the preliminary paper</ins>, <ins style="font-weight: bold; text-decoration: none;">focusing on the proposed work section. I also plan to look at the results on Brucella_suis_1330 in detail to evaluate correctness of contig placement given my repeat identification.</ins></div></td></tr> </table>

Sergek https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Serge-Report&diff=4547&oldid=prev 2009-02-12T23:11:57Z

<p></p> <p><b>New page</b></p><div>----<br /> February 16th, 2009</div>

Sergek