{"id":96,"date":"2016-12-23T15:36:01","date_gmt":"2016-12-23T14:36:01","guid":{"rendered":"http:\/\/staff.um.edu.mt\/jebej02\/blog\/?p=96"},"modified":"2023-02-16T13:29:40","modified_gmt":"2023-02-16T11:29:40","slug":"bioinformatics-starter-pack-getting-started-in-bioinformatics","status":"publish","type":"post","link":"https:\/\/bitsilla.com\/blog\/2016\/12\/bioinformatics-starter-pack-getting-started-in-bioinformatics\/","title":{"rendered":"Bioinformatics Starter Pack &#8211; Getting started in Bioinformatics"},"content":{"rendered":"<p>I often get the question &#8220;<em>I&#8217;m interested in Bioinformatics but how do I get started?<\/em>&#8220;. \u00a0That question can typically be answered with &#8220;<em>A google search<\/em>&#8220;, but that is true for most of the non-existential questions nowadays. \u00a0This post will give you pointers to material you need to cover to understand the basics of what this bioinformatics field is about. \u00a0Unfortunately, there currently is no undergraduate\/postgraduate course with focus on Bioinformatics (in Malta*) &#8211; so attending a series of (local) lectures is not an option presently. \u00a0Do not despair, plenty of material to go around.<\/p>\n<p><strong>Note: This material is not specific to one area in bioinformatics, e.g. genomics, but aims to give a general (soft) introduction to the field!<\/strong><\/p>\n<p><!--more--><\/p>\n<h1>Get Motivated!<\/h1>\n<p>First things, first. \u00a0<strong>Inspiration<\/strong>. \u00a0I remember watching this video and feeling close to Yegge&#8217;s philosophy, and even though this may superficially feel unconnected to the topic it explains the main reason\u00a0of why I got interested in bioinformatics.<\/p>\n<p><span class=\"embed-youtube\" style=\"text-align:center; display: block;\"><iframe loading=\"lazy\" class=\"youtube-player\" width=\"640\" height=\"360\" src=\"https:\/\/www.youtube.com\/embed\/vKmQW_Nkfk8?version=3&#038;rel=1&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;fs=1&#038;hl=en-US&#038;autohide=2&#038;wmode=transparent\" allowfullscreen=\"true\" style=\"border:0;\" sandbox=\"allow-scripts allow-same-origin allow-popups allow-presentation allow-popups-to-escape-sandbox\"><\/iframe><\/span><\/p>\n<h1>Articles<\/h1>\n<p>If you are computer scientists you need to bridge the biology gap. \u00a0Note that buying a Biology textbook is helpful, but not necessarily the quickest way to get you there. \u00a0The biology you&#8217;ll be dealing with is mostly molecular in nature (so that rules out anything you can see with your naked eye). \u00a0The following are a few excellent articles &#8220;for computer scientists&#8221; and non-CS people alike.<\/p>\n<ul>\n<li><a href=\"http:\/\/tandy.cs.illinois.edu\/Hunter_MolecularBiology.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">Molecular Biology for Computer Scientists<\/a>\u00a0(Lawrence Hunter, 46 pgs)<\/li>\n<li><a href=\"https:\/\/www.cs.ru.nl\/~perry\/hcc\/afstuderen\/docs\/Cohen-2004.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">Bioinformatics &#8211; An Introduction for Computer Scientists<\/a>\u00a0(Jacques Cohen, 37 pgs)<\/li>\n<li><a href=\"https:\/\/pdfs.semanticscholar.org\/dd25\/48c9f636a46abb3364dbf4de6183477f5061.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">What is Bioinformatics? An introduction and overview<\/a>\u00a0(Luscombe, Greenbaum, and Gerstein, 18 pgs)<\/li>\n<li><a href=\"https:\/\/brown-cs181-fall22.github.io\/quicklinks\/bioprimer.pdf\">A Biology Primer for Computer Scientists<\/a> (Preparata, 18 pgs)<\/li>\n<\/ul>\n<p>There are, of course, more &#8220;specific&#8221; bioinformatics general articles, e.g. <a href=\"http:\/\/www.nature.com\/nature\/journal\/v498\/n7453\/full\/498255a.html\" target=\"_blank\" rel=\"noopener noreferrer\">Big Data<\/a>, <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1093326313001137\" target=\"_blank\" rel=\"noopener noreferrer\">Cloud Computing<\/a>\u00a0(shameless plug) and <a href=\"http:\/\/bib.oxfordjournals.org\/content\/7\/1\/86.long\" target=\"_blank\" rel=\"noopener noreferrer\">Machine Learning<\/a>, but I will leave these for some future\u00a0post.<\/p>\n<h1>Online Courses<\/h1>\n<p>There is a great set of lectures by <a href=\"https:\/\/twitter.com\/benlangmead?lang=en\" target=\"_blank\" rel=\"noopener noreferrer\">Ben Langmead<\/a>\u00a0(Johns Hopkins University) from Coursera, titled &#8220;<a href=\"https:\/\/www.youtube.com\/playlist?list=PL2mpR0RYFQsBiCWVJSvVAO3OJ2t7DzoHA\" target=\"_blank\" rel=\"noopener noreferrer\">Algorithms for DNA Sequencing<\/a>&#8220;.\u00a0Last time I counted there were\u00a055 videos (each of variable length, 5 to 10 mins max). \u00a0During the summer months I organize sessions where we view a\u00a0handful of these at a go, and I answer questions related to the material presented. \u00a0I do this for fun, so holler (via comments below) if you are interested. \u00a0Notice that this\u00a0video lecture series is solely related to sequences.<\/p>\n<p>This section would not be complete without mentioning the <a href=\"https:\/\/www.coursera.org\/specializations\/bioinformatics\" target=\"_blank\" rel=\"noopener noreferrer\">bioinformatics specialization<\/a> in Coursera. \u00a0This is more general than Ben&#8217;s lectures, and it is also more involved with projects and deadlines. \u00a0This is a bit too &#8220;cartoonish&#8221; for my taste and perhaps aimed at a more playful audience.<\/p>\n<h1>Books<\/h1>\n<p>The good-ole coffee table balancer. \u00a0If you are old school and prefer a book, may I suggest Lesk&#8217;s <a href=\"https:\/\/amzn.to\/2Ch5joT\" rel=\"nofollow\">Introduction to Bioinformatics<\/a><img loading=\"lazy\" decoding=\"async\" style=\"border: none !important; margin: 0px !important;\" src=\"http:\/\/ir-uk.amazon-adsystem.com\/e\/ir?t=jpblog0a-21&amp;l=as2&amp;o=2&amp;a=0199651566\" alt=\"\" width=\"1\" height=\"1\" border=\"0\" \/>\u00a0(4th ed.)- which is the book which got me rolling in the area many editions and moons ago. \u00a0I always have a few copies in my office if you want to borrow one (mostly because these books are always on loan, and they are never sitting on the shelf). \u00a0Get in touch via comments below.<\/p>\n<figure id=\"attachment_100\" aria-describedby=\"caption-attachment-100\" style=\"width: 225px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/bitsilla.com\/blog\/wp-content\/uploads\/2016\/12\/IMG_20161222_133903.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-100\" src=\"http:\/\/bitsilla.com\/blog\/wp-content\/uploads\/2016\/12\/IMG_20161222_133903-225x300.jpg\" alt=\"\" width=\"225\" height=\"300\" srcset=\"https:\/\/bitsilla.com\/blog\/wp-content\/uploads\/2016\/12\/IMG_20161222_133903-225x300.jpg 225w, https:\/\/bitsilla.com\/blog\/wp-content\/uploads\/2016\/12\/IMG_20161222_133903-768x1024.jpg 768w\" sizes=\"auto, (max-width: 225px) 100vw, 225px\" \/><\/a><figcaption id=\"caption-attachment-100\" class=\"wp-caption-text\">Introduction to Bioinformatics, by Arthur Lesk<\/figcaption><\/figure>\n<h1>Next Steps&#8230;<\/h1>\n<p>So now you have things to watch and read. \u00a0In the next post of this series I will publish seminal bioinformatics papers, which cover most\u00a0areas of this exciting field. \u00a0Meanwhile, have some happy (Christmas) holidays!<\/p>\n<p>* This will change soon-ish, stay tuned.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I often get the question &#8220;I&#8217;m interested in Bioinformatics but how do I get started?&#8220;. \u00a0That question can typically be answered with &#8220;A google search&#8220;, but that is true for most of the non-existential questions nowadays. \u00a0This post will give you pointers to material you need to cover to understand the basics of what this [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[2],"tags":[],"class_list":["post-96","post","type-post","status-publish","format-standard","hentry","category-bioinformatics"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pap6Kd-1y","_links":{"self":[{"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/posts\/96","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/comments?post=96"}],"version-history":[{"count":6,"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/posts\/96\/revisions"}],"predecessor-version":[{"id":854,"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/posts\/96\/revisions\/854"}],"wp:attachment":[{"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/media?parent=96"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/categories?post=96"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/bitsilla.com\/blog\/wp-json\/wp\/v2\/tags?post=96"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}