{"id":2426,"date":"2009-05-18T16:01:54","date_gmt":"2009-05-18T16:01:54","guid":{"rendered":"https:\/\/blogs.mathworks.com\/pick\/2009\/05\/18\/for-bioinformaticistsor-gui-builders\/"},"modified":"2016-11-11T05:19:31","modified_gmt":"2016-11-11T10:19:31","slug":"for-bioinformaticistsor-gui-builders","status":"publish","type":"post","link":"https:\/\/blogs.mathworks.com\/pick\/2009\/05\/18\/for-bioinformaticistsor-gui-builders\/","title":{"rendered":"For Bioinformaticists&#8230;or GUI Builders"},"content":{"rendered":"<div class=\"alert alert-info\"> <span class=\"alert_icon icon-alert-info-reverse\"><\/span><p class=\"alert_heading\"><strong>Note<\/strong><\/p><p>The file submission referenced in this post is no longer available on File Exchange.<\/p><\/div>\r\n<div xmlns:mwsh=\"https:\/\/www.mathworks.com\/namespace\/mcode\/v1\/syntaxhighlight.dtd\" class=\"content\">\r\n   <introduction>\r\n      <p>This week's Pick: Primer Design Tool, by <a href=\"https:\/\/www.mathworks.com\/matlabcentral\/fileexchange\/authors\/23815\">Brian Madsen<\/a>.\r\n      <\/p>\r\n   <\/introduction>\r\n   <p>If you work in the field of bioinformatics, and especially if you do any primer design, you might be aware of a really nice demo that ships with the <a href=\"https:\/\/www.mathworks.com\/products\/bioinfo\/\">Bioinformatics Toolbox<\/a>, and that shows how to use our tools for that task.\r\n   <\/p>\r\n   <p>The script for <tt>primerdemo<\/tt> steps through the importing of data (from GenBank, for instance); calculating oligonucleotide properties; finding potential\r\n      forward and reverse primers, and filtering them based on (for example) GC content, melting temperature, and dimerization;\r\n      and visualizing and selecting primers based on user-specified criteria. This is all great stuff, if you are a bioinformaticist.\r\n   <\/p>\r\n   <p>Brian's \"Primer Design Tool\" takes all of these steps and wraps them very neatly into a GUI environment that makes it very\r\n      easy to modify constraints and to see the results of changing criteria. This is a very nice tool for folks who do primer design.\r\n   <\/p>\r\n   <p>However, what I <i>really<\/i> like about Brian's file is that it is a very useful demonstration of how converting code-based functionality to GUI-based\r\n      functionality can, with a little bit of effort, allow you to leverage the great demos that ship with our products. I don't\r\n      personally do a lot of primer design, for instance, but henceforth, whenever I am called upon to show this capability, I show\r\n      the in-product demo, and then I show Brian's GUI implementation of the functionality.\r\n   <\/p>\r\n   <p><img decoding=\"async\" vspace=\"5\" hspace=\"5\" src=\"https:\/\/blogs.mathworks.com\/pick\/..\/images\/pick\/primerdesign_png.png\"> <\/p>\r\n   <p>This is good stuff, even if you have no idea what an oligonucleotide is, or what primer design is all about.<\/p>\r\n   <p>Comments? Share them <a href=\"https:\/\/blogs.mathworks.com\/pick\/?p=2426#respond\">here<\/a>.\r\n   <\/p><script language=\"JavaScript\">\r\n<!--\r\n\r\n    function grabCode_3554c84e5357471cb6cb31a27b5a678a() {\r\n        \/\/ Remember the title so we can use it in the new page\r\n        title = document.title;\r\n\r\n        \/\/ Break up these strings so that their presence\r\n        \/\/ in the Javascript doesn't mess up the search for\r\n        \/\/ the MATLAB code.\r\n        t1='3554c84e5357471cb6cb31a27b5a678a ' + '##### ' + 'SOURCE BEGIN' + ' #####';\r\n        t2='##### ' + 'SOURCE END' + ' #####' + ' 3554c84e5357471cb6cb31a27b5a678a';\r\n    \r\n        b=document.getElementsByTagName('body')[0];\r\n        i1=b.innerHTML.indexOf(t1)+t1.length;\r\n        i2=b.innerHTML.indexOf(t2);\r\n \r\n        code_string = b.innerHTML.substring(i1, i2);\r\n        code_string = code_string.replace(\/REPLACE_WITH_DASH_DASH\/g,'--');\r\n\r\n        \/\/ Use \/x3C\/g instead of the less-than character to avoid errors \r\n        \/\/ in the XML parser.\r\n        \/\/ Use '\\x26#60;' instead of '<' so that the XML parser\r\n        \/\/ doesn't go ahead and substitute the less-than character. \r\n        code_string = code_string.replace(\/\\x3C\/g, '\\x26#60;');\r\n\r\n        author = 'Brett Shoelson';\r\n        copyright = 'Copyright 2009 The MathWorks, Inc.';\r\n\r\n        w = window.open();\r\n        d = w.document;\r\n        d.write('<pre>\\n');\r\n        d.write(code_string);\r\n\r\n        \/\/ Add author and copyright lines at the bottom if specified.\r\n        if ((author.length > 0) || (copyright.length > 0)) {\r\n            d.writeln('');\r\n            d.writeln('%%');\r\n            if (author.length > 0) {\r\n                d.writeln('% _' + author + '_');\r\n            }\r\n            if (copyright.length > 0) {\r\n                d.writeln('% _' + copyright + '_');\r\n            }\r\n        }\r\n\r\n        d.write('<\/pre>\\n');\r\n      \r\n      d.title = title + ' (MATLAB code)';\r\n      d.close();\r\n      }   \r\n      \r\n-->\r\n<\/script><p style=\"text-align: right; font-size: xx-small; font-weight:lighter;   font-style: italic; color: gray\"><br><a href=\"javascript:grabCode_3554c84e5357471cb6cb31a27b5a678a()\"><span style=\"font-size: x-small;        font-style: italic;\">Get \r\n            the MATLAB code \r\n            <noscript>(requires JavaScript)<\/noscript><\/span><\/a><br><br>\r\n      Published with MATLAB&reg; 7.8<br><\/p>\r\n<\/div>\r\n<!--\r\n3554c84e5357471cb6cb31a27b5a678a ##### SOURCE BEGIN #####\r\n%% For Bioinformaticists...or GUI Builders:\r\n% This week's Pick: <https:\/\/www.mathworks.com\/matlabcentral\/fileexchange\/11314 Primer Design Tool>, \r\n% by <https:\/\/www.mathworks.com\/matlabcentral\/fileexchange\/authors\/23815 Brian Madsen>. \r\n\r\n%%\r\n% If you work in the field of bioinformatics, and especially if you do any primer design,\r\n% you might be aware of a <https:\/\/www.mathworks.com\/products\/bioinfo\/demos.html?file=\/products\/demos\/shipping\/bioinfo\/primerdemo.html really nice demo> that ships with the <https:\/\/www.mathworks.com\/products\/bioinfo\/ Bioinformatics Toolbox>, and that shows how to use\r\n% our tools for that task.\r\n\r\n%%\r\n% The script for |primerdemo| steps through the importing of data\r\n% (from GenBank, for instance); calculating oligonucleotide\r\n% properties; finding potential forward and reverse primers, and\r\n% filtering them based on (for example) GC content, melting temperature,\r\n% and dimerization; and visualizing and selecting primers based\r\n% on user-specified criteria. This is all great stuff, if you are a bioinformaticist.\r\n\r\n%%\r\n% Brian's \"Primer Design Tool\" takes all of these steps and wraps them very neatly into a GUI environment\r\n% that makes it very easy to modify constraints and to see the\r\n% results of changing criteria. This is a very nice tool for\r\n% folks who do primer design.\r\n\r\n%%\r\n% However, what I _really_ like about Brian's file is that it is\r\n% a very useful demonstration of how converting code-based\r\n% functionality to GUI-based functionality can, with a little bit\r\n% of effort, allow you to leverage the great demos that ship with\r\n% our products. I don't personally do a lot of primer design, for\r\n% instance, but henceforth, whenever I am called upon to show\r\n% this capability, I show the in-product demo, and then I show\r\n% Brian's GUI implementation of the functionality.\r\n\r\n%%\r\n%\r\n% << https:\/\/blogs.mathworks.com\/pick\/..\/images\/pick\/primerdesign_png.png>>\r\n%\r\n%\r\n\r\n%%\r\n% This is good stuff, even if you have no idea what an\r\n% oligonucleotide is, or what primer design is all about. \r\n\r\n%%\r\n% Comments? Share them\r\n% <https:\/\/blogs.mathworks.com\/pick\/?p=2426#respond here>.\r\n##### SOURCE END ##### 3554c84e5357471cb6cb31a27b5a678a\r\n-->","protected":false},"excerpt":{"rendered":"<p> NoteThe file submission referenced in this post is no longer available on File Exchange.\r\n\r\n   \r\n      This week's Pick: Primer Design Tool, by Brian Madsen.\r\n      \r\n   \r\n   If you work in the... <a class=\"read-more\" href=\"https:\/\/blogs.mathworks.com\/pick\/2009\/05\/18\/for-bioinformaticistsor-gui-builders\/\">read more >><\/a><\/p>","protected":false},"author":34,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[16],"tags":[],"_links":{"self":[{"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/posts\/2426"}],"collection":[{"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/users\/34"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/comments?post=2426"}],"version-history":[{"count":1,"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/posts\/2426\/revisions"}],"predecessor-version":[{"id":8028,"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/posts\/2426\/revisions\/8028"}],"wp:attachment":[{"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/media?parent=2426"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/categories?post=2426"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.mathworks.com\/pick\/wp-json\/wp\/v2\/tags?post=2426"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}