{"id":161,"date":"2018-02-06T13:06:13","date_gmt":"2018-02-06T21:06:13","guid":{"rendered":"http:\/\/blogs.reed.edu\/compbio\/?p=161"},"modified":"2018-05-22T14:12:30","modified_gmt":"2018-05-22T21:12:30","slug":"week-14-2","status":"publish","type":"post","link":"https:\/\/blogs.reed.edu\/compbio\/2018\/02\/06\/week-14-2\/","title":{"rendered":"Week 14"},"content":{"rendered":"<p>At last week&#8217;s meeting, we dug into the computational portion of the project, discussing different ways we could run our algorithm on the gene lists and how that would affect our results. We also discussed a few different methods for running on our gene lists &#8211; one method involves a support vector machine and the other is an iterative method of computing scores, shown below.<\/p>\n<figure id=\"attachment_162\" aria-describedby=\"caption-attachment-162\" style=\"width: 292px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-162\" src=\"https:\/\/blogs.reed.edu\/compbio\/files\/2018\/02\/Screen-Shot-2018-02-06-at-12.46.51-PM-300x187.png\" alt=\"\" width=\"292\" height=\"182\" srcset=\"https:\/\/blogs.reed.edu\/compbio\/files\/2018\/02\/Screen-Shot-2018-02-06-at-12.46.51-PM-300x187.png 300w, https:\/\/blogs.reed.edu\/compbio\/files\/2018\/02\/Screen-Shot-2018-02-06-at-12.46.51-PM.png 394w\" sizes=\"auto, (max-width: 292px) 85vw, 292px\" \/><figcaption id=\"caption-attachment-162\" class=\"wp-caption-text\">Murali et al. Network- based prediction and analysis of hiv dependency factors. PLOS Computational<br \/>Biology, 2011.<\/figcaption><\/figure>\n<p>Alex was able to track down some software for the former method from the <a href=\"http:\/\/asd.princeton.edu\/\">autism paper<\/a> that inspired our project. One of our tasks was to try to get this software to work on our current gene lists &#8211; unfortunately, we hit a bit of a wall with this method.<\/p>\n<p>For the second method, we were able to successfully run it on Alex&#8217;s gene list. I also had the task of running the iterative method on a small toy example, which was a small graph consisting of 10 nodes, 11 edges, 1 positive, and 1 negative. Anna informed me that when she did it, the scores converged after about 27 time steps, which matches the results that I got. We will go over the results in this week&#8217;s meeting and discuss what our goals for this week are.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>At last week&#8217;s meeting, we dug into the computational portion of the project, discussing different ways we could run our algorithm on the gene lists and how that would affect our results. We also discussed a few different methods for running on our gene lists &#8211; one method involves a support vector machine and the &hellip; <a href=\"https:\/\/blogs.reed.edu\/compbio\/2018\/02\/06\/week-14-2\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Week 14&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1583,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7,8,1],"tags":[],"class_list":["post-161","post","type-post","status-publish","format-standard","hentry","category-creu","category-schizophrenia","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/161","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/users\/1583"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/comments?post=161"}],"version-history":[{"count":2,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/161\/revisions"}],"predecessor-version":[{"id":168,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/161\/revisions\/168"}],"wp:attachment":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/media?parent=161"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/categories?post=161"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/tags?post=161"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}