{"version":"https://jsonfeed.org/version/1.1","title":"Computational Bioinformatics","description":"Recent content on Computational Bioinformatics","home_page_url":"https://computationalbioinformatics.com/","feed_url":"https://computationalbioinformatics.com/index.json","language":"en-GB","favicon":"https://computationalbioinformatics.com/logo.png","authors":[{"name":"Oliver Bonham-Carter","url":"https://oliverbonhamcarter.com"}],"items":[{"title":"Assignments","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/assignments/","url":"https://computationalbioinformatics.com/assignments/","content_html":"\u003ch2 id=\"assignments-at-a-glance\" class=\"anchor-header\"\u003eAssignments at a Glance \u003ca class=\"anchor-link\" href=\"#assignments-at-a-glance\" aria-label=\"Assignments at a Glance\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cp\u003eAll assignments are hosted in the course GitHub organization. Use the cards below to jump to each repository.\u003c/p\u003e\n\u003cdiv class=\"feature-grid\"\u003e\u003cdiv class=\"feature-card\"\u003e\u003ch3 id=\"assignment-1\" class=\"anchor-header\"\u003eAssignment 1 \u003ca class=\"anchor-link\" href=\"#assignment-1\" aria-label=\"Assignment 1\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h3\u003e\n\u003cp\u003eResearching and reporting on bioinformatics research tools (I).\u003c/p\u003e\n\u003cp\u003e\u003ca class=\"button button--small button--outline\" href=\"https://github.com/Computational-Bioinformatics/01_lab\"\u003eRepository\u003c/a\u003e\u003c/p\u003e\n\u003ch4 id=\"objectives\" class=\"anchor-header\"\u003eObjectives \u003ca class=\"anchor-link\" href=\"#objectives\" aria-label=\"Objectives\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cul\u003e\n\u003cli\u003eUse JupyterLite to pull, complete, and submit homework.\u003c/li\u003e\n\u003cli\u003eUse GitHub and \u003ccode\u003egit\u003c/code\u003e to manage submissions.\u003c/li\u003e\n\u003cli\u003eMake a basic edit to a Python program.\u003c/li\u003e\n\u003cli\u003eResearch and report on bioinformatics tools.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/div\u003e\n\u003cdiv class=\"feature-card\"\u003e\u003ch3 id=\"assignment-2\" class=\"anchor-header\"\u003eAssignment 2 \u003ca class=\"anchor-link\" href=\"#assignment-2\" aria-label=\"Assignment 2\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h3\u003e\n\u003cp\u003eCentral Dogma of Biology and Bioinformatics.\u003c/p\u003e\n\u003cp\u003e\u003ca class=\"button button--small button--outline\" href=\"https://github.com/Computational-Bioinformatics/02_activity_pythonTutorials_starter\"\u003eRepository\u003c/a\u003e\u003c/p\u003e\n\u003ch4 id=\"objectives\" class=\"anchor-header\"\u003eObjectives \u003ca class=\"anchor-link\" href=\"#objectives\" aria-label=\"Objectives\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cul\u003e\n\u003cli\u003eConnect the Central Dogma of Biology to bioinformatics practice.\u003c/li\u003e\n\u003cli\u003eExplore Python debugging and problem-solving strategies.\u003c/li\u003e\n\u003cli\u003eRun sequence experiments using starter code.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/div\u003e\n\u003cdiv class=\"feature-card\"\u003e\u003ch3 id=\"assignment-3\" class=\"anchor-header\"\u003eAssignment 3 \u003ca class=\"anchor-link\" href=\"#assignment-3\" aria-label=\"Assignment 3\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h3\u003e\n\u003cp\u003eResearching and reporting on bioinformatics research tools (II).\u003c/p\u003e\n\u003cp\u003e\u003ca class=\"button button--small button--outline\" href=\"https://github.com/Computational-Bioinformatics/03_lab\"\u003eRepository\u003c/a\u003e\u003c/p\u003e\n\u003ch4 id=\"objectives\" class=\"anchor-header\"\u003eObjectives \u003ca class=\"anchor-link\" href=\"#objectives\" aria-label=\"Objectives\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cul\u003e\n\u003cli\u003eIdentify tools for specific research tasks.\u003c/li\u003e\n\u003cli\u003ePresent and explain a tool to peers.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/div\u003e\n\u003cdiv class=\"feature-card\"\u003e\u003ch3 id=\"assignment-4\" class=\"anchor-header\"\u003eAssignment 4 \u003ca class=\"anchor-link\" href=\"#assignment-4\" aria-label=\"Assignment 4\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h3\u003e\n\u003cp\u003eWhat Is This Sequence?\u003c/p\u003e\n\u003cp\u003e\u003ca class=\"button button--small button--outline\" href=\"https://github.com/Computational-Bioinformatics/04_lab_starter\"\u003eRepository\u003c/a\u003e\u003c/p\u003e\n\u003ch4 id=\"objectives\" class=\"anchor-header\"\u003eObjectives \u003ca class=\"anchor-link\" href=\"#objectives\" aria-label=\"Objectives\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cul\u003e\n\u003cli\u003eInvestigate sequence data using online and local analysis tools.\u003c/li\u003e\n\u003cli\u003eInterpret software output to identify sequence origins.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/div\u003e\n\u003cdiv class=\"feature-card\"\u003e\u003ch3 id=\"assignment-5\" class=\"anchor-header\"\u003eAssignment 5 \u003ca class=\"anchor-link\" href=\"#assignment-5\" aria-label=\"Assignment 5\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h3\u003e\n\u003cp\u003eInvestigating Online Tools.\u003c/p\u003e\n\u003cp\u003e\u003ca class=\"button button--small button--outline\" href=\"https://github.com/Computational-Bioinformatics/05_lab\"\u003eRepository\u003c/a\u003e\u003c/p\u003e\n\u003ch4 id=\"objectives\" class=\"anchor-header\"\u003eObjectives \u003ca class=\"anchor-link\" href=\"#objectives\" aria-label=\"Objectives\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cul\u003e\n\u003cli\u003eRead literature and summarize relevant science.\u003c/li\u003e\n\u003cli\u003eInstall and apply software tools to datasets.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/div\u003e\n\u003cdiv class=\"feature-card\"\u003e\u003ch3 id=\"assignment-6\" class=\"anchor-header\"\u003eAssignment 6 \u003ca class=\"anchor-link\" href=\"#assignment-6\" aria-label=\"Assignment 6\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h3\u003e\n\u003cp\u003eEthical Topics in Bioinformatics.\u003c/p\u003e\n\u003cp\u003e\u003ca class=\"button button--small button--outline\" href=\"https://github.com/Computational-Bioinformatics/Final_Project\"\u003eRepository\u003c/a\u003e\u003c/p\u003e\n\u003ch4 id=\"objectives\" class=\"anchor-header\"\u003eObjectives \u003ca class=\"anchor-link\" href=\"#objectives\" aria-label=\"Objectives\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cul\u003e\n\u003cli\u003eRead literature and gather supporting evidence.\u003c/li\u003e\n\u003cli\u003eIdentify ethical dilemmas in bioinformatics research.\u003c/li\u003e\n\u003cli\u003eEvaluate outcomes in terms of fairness and accountability.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\n"},{"title":"Bioinformatics Resources","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/resources/bioinformatics_resources/","url":"https://computationalbioinformatics.com/resources/bioinformatics_resources/","content_html":"\u003cp\u003eWelcome to a resources page for bioinformatics research. Here you will find links for data, tools, tutorials, and related resources that may be helpful to your work.\u003c/p\u003e\n\u003ch2 id=\"software-and-installations\" class=\"anchor-header\"\u003eSoftware and installations \u003ca class=\"anchor-link\" href=\"#software-and-installations\" aria-label=\"Software and installations\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://posit.co/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eRStudio\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://cran.rstudio.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eR Programming Language\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.python.org/downloads/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePython Programming Language\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://mac.github.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGit for Mac\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://windows.github.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGit for Windows\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://git-scm.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGit for all platforms\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.pythonforbiologists.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePython for Biologists\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://biopython.org/DIST/docs/tutorial/Tutorial.html\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eBioPython\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"python-programming-resources\" class=\"anchor-header\"\u003ePython programming resources \u003ca class=\"anchor-link\" href=\"#python-programming-resources\" aria-label=\"Python programming resources\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003ePlay with code from W3\u0026rsquo;s \u003ca href=\"https://www.w3schools.com/python/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePython Tutorial\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eWrite code locally using \u003ca href=\"http://oliverbonhamcarter.com/live/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eJupyter Interactive Python\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eThink Python by Allen B. Downey: \u003ca href=\"https://greenteapress.com/wp/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePublisher Website\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.python.org/downloads/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePython Programming Language\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.jdoodle.com/execute-r-online/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eOnline R programming\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"articles\" class=\"anchor-header\"\u003eArticles \u003ca class=\"anchor-link\" href=\"#articles\" aria-label=\"Articles\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.markdownguide.org/getting-started/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGetting started with Markdown\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"tutorials\" class=\"anchor-header\"\u003eTutorials \u003ca class=\"anchor-link\" href=\"#tutorials\" aria-label=\"Tutorials\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/playlist?list=PLsYZRXov75ZHSwWiCk0-jd1RcTuu_-zmD\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eAllegheny College Department of Computer Science tutorials\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/playlist?list=PLRqwX-V7Uu6ZF9C0YMKuns9sLDzK6zoiV\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eCoding Train\u0026rsquo;s Git and GitHub for Poets\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.digitalocean.com/community/tutorials/how-to-install-git-on-ubuntu-20-04\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eSetting Up Git on Linux\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://swcarpentry.github.io/git-novice/02-setup/index.html\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eSetting up Git\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://code.visualstudio.com/docs/python/python-tutorial\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGetting Started with Python in VS Code\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://towardsthecloud.com/best-vscode-extensions-python\" target=\"_blank\" rel=\"noopener noreferrer\"\u003e11 Best VS Code extensions for Python (2022)\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.ssh.com/ssh/keygen/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eSSH keys\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/watch?v=qEPjUGQFmzQ\u0026amp;list=PLsYZRXov75ZHSwWiCk0-jd1RcTuu_-zmD\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eLuman\u0026rsquo;s SSH keys video tutorial\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"tools-and-learning-links\" class=\"anchor-header\"\u003eTools and learning links \u003ca class=\"anchor-link\" href=\"#tools-and-learning-links\" aria-label=\"Tools and learning links\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.biointeractive.org/classroom-resources/virus-explorer\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eVirus Explorer\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://tcoffee.crg.cat/apps/tcoffee/tutorial.html\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eTCoffee tutorial\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/watch?v=TPRoLreU9lA\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eHidden Markov Models (YouTube)\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://media.hhmi.org/biointeractive/films/Double_Helix.html\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eThe Double Helix (documentary, 17 mins)\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.biointeractive.org/classroom-resources/chemical-structure-dna\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eThe Chemical Structure of DNA\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/watch?v=o_-6JXLYS-k\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eThe Structure of DNA\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/watch?v=qWZYpHSXvJo\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eDefinition of 5\u0026rsquo; and 3\u0026rsquo; end of DNA (video)\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/watch?v=vP8-5Bhd2ag\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eWhat happens when your DNA is damaged?\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/watch?v=BBI7GoIyoog\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eMutations and Natural Selection\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.youtube.com/watch?v=NDIJexTT9j0\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eProtein synthesis animation\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://www.lungendothelialcellatlas.com\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eLung Endothelial Cell Atlas\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://www.copdcellatlas.com\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eCOPD Cell Atlas\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://www.covidcellatlas.com\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eCOVID Cell Atlas\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://www.ipfcellatlas.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eIdiopathic Pulmonary Fibrosis Cell Atlas\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.kazusa.or.jp/codon/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eCodon Usage Database\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://card.mcmaster.ca/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eComprehensive Antibiotic Resistance Database\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://card.mcmaster.ca/ontology/36514\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eermB anti resistance gene\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://web.expasy.org/sim/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eSIM alignment tool\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://card.mcmaster.ca/analyze\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eBlast analysis\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://www.diamondsearch.org/index.php\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eDiamond (BLAST alternative)\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://hmmer.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eHMMER\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://geneontology.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGene Ontology Resource\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://www.pantherdb.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePanther Classification System\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://blast.ncbi.nlm.nih.gov/Blast.cgi\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eBLAST\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.genome.jp/tools/egassembler/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eEGassembler\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://elm.eu.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eELM tool kit\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://www.rcsb.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eProtein Data Bank\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://open.predictprotein.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePredict protein\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://string-db.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eString database\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://prosite.expasy.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eProsite: domains, families, and functional sites\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://experiments.mostafa.io/public/needleman-wunsch/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eNeedleman-Wunsch algorithm demo\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://ugene.net/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eUGENE\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://thecellmap.org/?q=pex6\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eThe Cell Map\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://amigo.geneontology.org/amigo/landing\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eAmiGo Gene Ontology\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://ghr.nlm.nih.gov/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGenetics Home Reference\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://nesg.org/galleries.html\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eNortheast Structural Genomics Consortium\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://modbase.compbio.ucsf.edu/modeval/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eModEval\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://pymol.org/2/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePyMol\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://qiime2.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eQiime2\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://go.drugbank.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eDrugBank\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"http://bioinf.uni-greifswald.de/augustus/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eAugustus gene prediction\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"research-organizations\" class=\"anchor-header\"\u003eResearch organizations \u003ca class=\"anchor-link\" href=\"#research-organizations\" aria-label=\"Research organizations\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://knowyourdna.com/cataracts-and-genetics/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eCataracts and Genetics\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.genome.gov/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eNational Human Genome Research Institute\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.molgen.mpg.de/2168/en\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eMax Planck Institute for Molecular Genetics\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003chr\u003e\n\u003ch3 id=\"note\" class=\"anchor-header\"\u003eNote \u003ca class=\"anchor-link\" href=\"#note\" aria-label=\"Note\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h3\u003e\n\u003cp\u003eIf you find a good link for bioinformatics research that you believe would fit nicely here, please let me know.\u003c/p\u003e\n"},{"title":"Career Paths","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/resources/career-paths/","url":"https://computationalbioinformatics.com/resources/career-paths/","content_html":"\u003ch1 id=\"bioinformatics-career-paths\" class=\"anchor-header\"\u003eBioinformatics Career Paths \u003ca class=\"anchor-link\" href=\"#bioinformatics-career-paths\" aria-label=\"Bioinformatics Career Paths\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h1\u003e\n\u003cp\u003eThis page gives a quick overview of roles, skills, and entry points in computational biology and bioinformatics.\u003c/p\u003e\n\u003ch2 id=\"roles-you-might-see\" class=\"anchor-header\"\u003eRoles you might see \u003ca class=\"anchor-link\" href=\"#roles-you-might-see\" aria-label=\"Roles you might see\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eBioinformatics Analyst\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003eFocus: data cleaning, pipelines, and reports.\u003c/li\u003e\n\u003cli\u003eTypical tools: Python, R, Bash, SQL, workflow tools.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eComputational Biologist\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003eFocus: algorithm development, research modeling, and analysis.\u003c/li\u003e\n\u003cli\u003eTypical tools: Python, R, statistics, machine learning basics.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eGenomics Data Scientist\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003eFocus: high-throughput sequencing, ML, and reproducible analytics.\u003c/li\u003e\n\u003cli\u003eTypical tools: Python, R, ML libraries, cloud platforms.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eBioinformatics Software Engineer\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003eFocus: production software, APIs, and data systems.\u003c/li\u003e\n\u003cli\u003eTypical tools: Python, Go, Java, Docker, CI/CD.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eClinical Genomics Specialist\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003eFocus: variant interpretation, regulated pipelines, clinical reporting.\u003c/li\u003e\n\u003cli\u003eTypical tools: standards (HGVS), ClinVar, pipelines, QC.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"core-skills-to-build-in-this-course\" class=\"anchor-header\"\u003eCore skills to build in this course \u003ca class=\"anchor-link\" href=\"#core-skills-to-build-in-this-course\" aria-label=\"Core skills to build in this course\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003eSequence alignment, assembly, and annotation basics.\u003c/li\u003e\n\u003cli\u003eData handling and reproducible analysis with notebooks.\u003c/li\u003e\n\u003cli\u003eClear reporting: methods, results, and limitations.\u003c/li\u003e\n\u003cli\u003eEthical data use, privacy, and bias awareness.\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"how-to-prepare\" class=\"anchor-header\"\u003eHow to prepare \u003ca class=\"anchor-link\" href=\"#how-to-prepare\" aria-label=\"How to prepare\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003eBuild a small portfolio: 2 to 3 notebooks or reports.\u003c/li\u003e\n\u003cli\u003ePractice writing short analysis summaries for non-technical readers.\u003c/li\u003e\n\u003cli\u003eLearn the command line and Git basics.\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"where-to-look-for-roles\" class=\"anchor-header\"\u003eWhere to look for roles \u003ca class=\"anchor-link\" href=\"#where-to-look-for-roles\" aria-label=\"Where to look for roles\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003eAcademic labs and research institutes.\u003c/li\u003e\n\u003cli\u003eBiotech and pharma companies.\u003c/li\u003e\n\u003cli\u003eHospitals and clinical genomics labs.\u003c/li\u003e\n\u003cli\u003eGovernment or public health agencies.\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"example-job-boards\" class=\"anchor-header\"\u003eExample job boards \u003ca class=\"anchor-link\" href=\"#example-job-boards\" aria-label=\"Example job boards\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.iscb.org/careers\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.iscb.org/careers\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.ebi.ac.uk/careers\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.ebi.ac.uk/careers\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.nature.com/naturecareers\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.nature.com/naturecareers\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.linkedin.com/jobs/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.linkedin.com/jobs/\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"suggested-class-activity\" class=\"anchor-header\"\u003eSuggested class activity \u003ca class=\"anchor-link\" href=\"#suggested-class-activity\" aria-label=\"Suggested class activity\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003eFind one job posting and map the required skills to course topics.\u003c/li\u003e\n\u003c/ul\u003e\n"},{"title":"Data Sources","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/resources/data-sources/","url":"https://computationalbioinformatics.com/resources/data-sources/","content_html":"\u003ch1 id=\"data-sources-for-bioinformatics\" class=\"anchor-header\"\u003eData Sources for Bioinformatics \u003ca class=\"anchor-link\" href=\"#data-sources-for-bioinformatics\" aria-label=\"Data Sources for Bioinformatics\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h1\u003e\n\u003cp\u003eThis page lists reliable datasets and databases for sequence, structure, expression, and pathway analysis. Each resource includes common use cases and citation guidance.\u003c/p\u003e\n\u003ch2 id=\"core-sequence-and-genome-resources\" class=\"anchor-header\"\u003eCore sequence and genome resources \u003ca class=\"anchor-link\" href=\"#core-sequence-and-genome-resources\" aria-label=\"Core sequence and genome resources\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eNCBI\u003c/strong\u003e (GenBank, RefSeq, GEO, SRA)\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.ncbi.nlm.nih.gov/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.ncbi.nlm.nih.gov/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: general sequence records, curated reference genomes, gene expression data, and raw reads.\u003c/li\u003e\n\u003cli\u003eCite: follow the dataset accession page; many provide a preferred citation.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eENA\u003c/strong\u003e (European Nucleotide Archive)\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.ebi.ac.uk/ena/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.ebi.ac.uk/ena/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: raw sequencing data and assembled sequences.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eEnsembl\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.ensembl.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.ensembl.org/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: genome browsers, annotations, comparative genomics.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eUCSC Genome Browser\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://genome.ucsc.edu/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://genome.ucsc.edu/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: visualization, genome tracks, custom annotations.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"protein-structure-and-function\" class=\"anchor-header\"\u003eProtein, structure, and function \u003ca class=\"anchor-link\" href=\"#protein-structure-and-function\" aria-label=\"Protein, structure, and function\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eUniProt\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.uniprot.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.uniprot.org/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: protein sequences, function, and cross references.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ePDB\u003c/strong\u003e (Protein Data Bank)\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.rcsb.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.rcsb.org/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: 3D protein and nucleic acid structures.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eAlphaFold DB\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://alphafold.ebi.ac.uk/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://alphafold.ebi.ac.uk/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: predicted protein structures.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eInterPro\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.ebi.ac.uk/interpro/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.ebi.ac.uk/interpro/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: domains, families, and functional analysis.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"expression-variation-and-pathways\" class=\"anchor-header\"\u003eExpression, variation, and pathways \u003ca class=\"anchor-link\" href=\"#expression-variation-and-pathways\" aria-label=\"Expression, variation, and pathways\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eGEO\u003c/strong\u003e (Gene Expression Omnibus)\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.ncbi.nlm.nih.gov/geo/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.ncbi.nlm.nih.gov/geo/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: microarray and RNA-seq expression datasets.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eGTEx\u003c/strong\u003e (Genotype-Tissue Expression)\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://gtexportal.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://gtexportal.org/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: tissue-specific expression patterns.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eClinVar\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.ncbi.nlm.nih.gov/clinvar/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.ncbi.nlm.nih.gov/clinvar/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: variant clinical significance.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eKEGG\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://www.kegg.jp/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://www.kegg.jp/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: pathways, reactions, and pathway maps.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eReactome\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://reactome.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://reactome.org/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eUse for: curated biological pathways.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"citation-tips\" class=\"anchor-header\"\u003eCitation tips \u003ca class=\"anchor-link\" href=\"#citation-tips\" aria-label=\"Citation tips\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003ePrefer accession numbers over informal dataset names.\u003c/li\u003e\n\u003cli\u003eCheck the dataset page for a citation or DOI.\u003c/li\u003e\n\u003cli\u003eInclude database name and version when available.\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"suggested-class-activities\" class=\"anchor-header\"\u003eSuggested class activities \u003ca class=\"anchor-link\" href=\"#suggested-class-activities\" aria-label=\"Suggested class activities\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003ePick one database and write a short guide: what it stores, how to search it, and how to cite it.\u003c/li\u003e\n\u003cli\u003eCompare two sources for the same gene or protein and note differences in annotation.\u003c/li\u003e\n\u003c/ul\u003e\n"},{"title":"Policy","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/policy/","url":"https://computationalbioinformatics.com/policy/","content_html":"\u003ch2 id=\"policies\" class=\"anchor-header\"\u003ePolicies \u003ca class=\"anchor-link\" href=\"#policies\" aria-label=\"Policies\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cdetails\u003e\n\u003csummary\u003eGrading\u003c/summary\u003e\n\u003cp\u003eThe grade that a student receives in this class will be based on the following categories. All percentages are approximate and may change during the academic semester.\u003c/p\u003e\n\u003ctable\u003e\n  \u003cthead\u003e\n      \u003ctr\u003e\n          \u003cth style=\"text-align: left\"\u003eCategory\u003c/th\u003e\n          \u003cth style=\"text-align: left\"\u003ePercentage\u003c/th\u003e\n          \u003cth style=\"text-align: left\"\u003eAssessment metric\u003c/th\u003e\n      \u003c/tr\u003e\n  \u003c/thead\u003e\n  \u003ctbody\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eClass Participation\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e10%\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003echeck mark grade\u003c/td\u003e\n      \u003c/tr\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eExams\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e20%\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eletter grade\u003c/td\u003e\n      \u003c/tr\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eLab Assignments\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e40%\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eletter grade\u003c/td\u003e\n      \u003c/tr\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eFinal Project\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e30%\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eletter grade\u003c/td\u003e\n      \u003c/tr\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eTotal\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e100%\u003c/td\u003e\n          \u003ctd\u003e\u003c/td\u003e\n      \u003c/tr\u003e\n  \u003c/tbody\u003e\n\u003c/table\u003e\n\u003ch4 id=\"grading-scale\" class=\"anchor-header\"\u003eGrading Scale \u003ca class=\"anchor-link\" href=\"#grading-scale\" aria-label=\"Grading Scale\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003ctable\u003e\n  \u003cthead\u003e\n      \u003ctr\u003e\n          \u003cth style=\"text-align: left\"\u003eLetter\u003c/th\u003e\n          \u003cth style=\"text-align: left\"\u003eRange\u003c/th\u003e\n          \u003cth style=\"text-align: left\"\u003eLetter\u003c/th\u003e\n          \u003cth style=\"text-align: left\"\u003eRange\u003c/th\u003e\n          \u003cth style=\"text-align: left\"\u003eLetter\u003c/th\u003e\n          \u003cth style=\"text-align: left\"\u003eRange\u003c/th\u003e\n      \u003c/tr\u003e\n  \u003c/thead\u003e\n  \u003ctbody\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eA\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e96 - 100\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eA-\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e90 - 95.9\u003c/td\u003e\n          \u003ctd\u003e\u003c/td\u003e\n          \u003ctd\u003e\u003c/td\u003e\n      \u003c/tr\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eB+\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e87 - 89.9\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eB\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e83 - 86.9\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eB-\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e80 - 82.9\u003c/td\u003e\n      \u003c/tr\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eC+\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e77 - 79.9\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eC\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e73 - 76.9\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eC-\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e70 - 72.9\u003c/td\u003e\n      \u003c/tr\u003e\n      \u003ctr\u003e\n          \u003ctd style=\"text-align: left\"\u003eD+\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e67 - 69.9\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eD\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e63 - 66.9\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003eF\u003c/td\u003e\n          \u003ctd style=\"text-align: left\"\u003e59.9 and below\u003c/td\u003e\n      \u003c/tr\u003e\n  \u003c/tbody\u003e\n\u003c/table\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eDefinitions of Grading Categories\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eClass Participation\u003c/strong\u003e: Active participation during class sessions, including questions, exercises, presentations, and leading discussions.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eExams\u003c/strong\u003e: Cover material in their associated module(s). Dates are announced at least one week in advance.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eLaboratory Assignments\u003c/strong\u003e: Explore concepts, tools, and techniques in bioinformatics. Assignments may be completed in teams and may require presentations or demonstrations.\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eFinal Project\u003c/strong\u003e: A complete bioinformatics solution to a specific problem. Details are provided approximately two months before finals.\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eAssignment Submission\u003c/summary\u003e\n\u003cp\u003eWe will use GitHub Classroom to collect assignments. It is expected that you can use \u003ccode\u003egit\u003c/code\u003e to submit your work. Ask peers, Technology Leaders, or the instructor if you need help.\u003c/p\u003e\n\u003cp\u003eAll assignments have a due date and are submitted at the beginning of the lab session. Late submissions are accepted for up to one week with a 15% penalty and must be submitted at the beginning of the session one week after the due date.\u003c/p\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eExtensions\u003c/summary\u003e\n\u003cp\u003eNo assignments are accepted after the late deadline without prior arrangements. If you request an extension, email the instructor before the due date with a valid reason. Extensions are 24 hours and are granted at the instructor\u0026rsquo;s discretion.\u003c/p\u003e\n\u003cp\u003eThe submission of homework includes the Honor Code pledge. Group assignments require a one-page reflection describing each member\u0026rsquo;s contribution.\u003c/p\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eExtenuating Circumstances\u003c/summary\u003e\n\u003cp\u003eIf circumstances interfere with your ability to prepare for class or complete assignments, contact the instructor immediately. You may also find these campus resources helpful:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://sites.allegheny.edu/learningcommons/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eMaytum Center for Student Success\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://sites.allegheny.edu/learningcommons/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eAllegheny College Counseling Center\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://sites.allegheny.edu/healthcenter/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eThe Winslow Health Center\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://sites.allegheny.edu/studentlife/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eStudent Life\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eCommunication\u003c/summary\u003e\n\u003cp\u003eWe will use email, Discord, and the GitHub issue tracker. Install the Discord app to receive timely updates.\u003c/p\u003e\n\u003cp\u003eThe course website stores the syllabus, schedule, and information about the \u003ccode\u003eclassDocs/\u003c/code\u003e repository. Grades are communicated through a Gradebook GitHub repository.\u003c/p\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eBring Your Own Computer\u003c/summary\u003e\n\u003cp\u003eThe Department of Computer Science does not provide student machines. Bring a wifi-ready device to class. If the class meets online, make sure your system supports Zoom and other required services.\u003c/p\u003e\n\u003cp\u003eYou will be asked to install software during the semester, including:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eGit and GitHub\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://code.visualstudio.com/download\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eVS Code\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.docker.com\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eDocker\u003c/a\u003e\n\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://docs.docker.com/get-docker/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eInstalling Docker\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://www.docker.com/101-tutorial\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eBasic tutorial from Docker\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://labs.play-with-docker.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ePlay with Docker\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eSpecial Needs and Disability Services\u003c/summary\u003e\n\u003cp\u003eThe Americans with Disabilities Act (ADA) requires reasonable accommodations. Students who need accommodations are encouraged to contact Disability Services at 332-2898. Disability Services is part of the Learning Commons in Pelletier Library.\u003c/p\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eHonor Code\u003c/summary\u003e\n\u003cp\u003eThe Academic Honor Program applies to all work submitted for academic credit and includes examinations, laboratory assignments, and the final project. Each student acknowledges the Honor Code pledge:\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eI hereby recognize and pledge to fulfill my responsibilities, as defined in the Honor Code, and to maintain the integrity of both myself and the College community as a whole.\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003eDiscussing work with classmates is encouraged, but submitting work identical to others is a violation. More information is available at the \u003ca href=\"https://sites.allegheny.edu/studentsuccess/academic-honor-program/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eMaytum Center for Student Success\u003c/a\u003e\n.\u003c/p\u003e\n\n\u003c/details\u003e\n\n"},{"title":"Schedule","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/schedule/","url":"https://computationalbioinformatics.com/schedule/","content_html":"\u003ch2 id=\"schedule\" class=\"anchor-header\"\u003eSchedule \u003ca class=\"anchor-link\" href=\"#schedule\" aria-label=\"Schedule\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cp\u003eBelow is a tentative schedule of covered topics and associated activities. The schedule is subject to change with the addition of guest appearances.\u003c/p\u003e\n\u003cdetails\u003e\n\u003csummary\u003eWeek 1\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Introduction to the course and careers.\u003c/li\u003e\n\u003cli\u003eLab: No lab.\u003c/li\u003e\n\u003cli\u003eReading: Read the syllabus.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/career-paths/\"\u003eCareer Paths\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 2\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: DNA basics, Central Dogma, replication, Activity 01.\u003c/li\u003e\n\u003cli\u003eLab: Software tools.\u003c/li\u003e\n\u003cli\u003eReading: Chapter 1.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/tools-environments/\"\u003eTools and Environments\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 3\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: BioPython basics, Activity 02.\u003c/li\u003e\n\u003cli\u003eLab: BioPython and silent mutations.\u003c/li\u003e\n\u003cli\u003eReading: Chapter 1.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/assignments/\"\u003eAssignments\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 4\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Reading frames, mutations, sequence alignment, Activity 03.\u003c/li\u003e\n\u003cli\u003eLab: Tool intro and presentation.\u003c/li\u003e\n\u003cli\u003eReading: Chapters 2 and 3.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/data-sources/\"\u003eData Sources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 5\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Sequence alignment and Needleman-Wunsch (global alignment).\u003c/li\u003e\n\u003cli\u003eLab: No new assignment.\u003c/li\u003e\n\u003cli\u003eReading: Chapter 3.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/bioinformatics_resources/\"\u003eBioinformatics Resources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 6\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Biopython and sequence alignment, Activity 04.\u003c/li\u003e\n\u003cli\u003eLab: Sequence analysis.\u003c/li\u003e\n\u003cli\u003eReading: Chapters 3 and 4.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/assignments/\"\u003eAssignments\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 7\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Fall break, no class.\u003c/li\u003e\n\u003cli\u003eLab: No lab.\u003c/li\u003e\n\u003cli\u003eActivity: Activity 05 BuildADatabase.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/assignments/\"\u003eAssignments\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 8\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: BLAST and protein BLAST.\u003c/li\u003e\n\u003cli\u003eLab: Article and tool.\u003c/li\u003e\n\u003cli\u003eReading: Chapters 4 and 5.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/bioinformatics_resources/\"\u003eBioinformatics Resources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 9\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Substitution matrices (PAM, BLOSUM). Test week: Activity 06 (video).\u003c/li\u003e\n\u003cli\u003eLab: See last week\u0026rsquo;s lab.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/assignments/\"\u003eAssignments\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 10\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Gene assembly, \u003ca href=\"https://classroom.github.com/a/KHpM-Nhi\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eActivity 07\u003c/a\u003e\n.\u003c/li\u003e\n\u003cli\u003eLab: \u003ca href=\"https://classroom.github.com/a/VNZ2geci\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eEthics in Bioinformatics Research\u003c/a\u003e\n.\u003c/li\u003e\n\u003cli\u003eReading: Chapters 8 and 9.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/writing/\"\u003eWriting Resources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 11\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Protein research websites, Activity 08.\u003c/li\u003e\n\u003cli\u003eLab: Hand out.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/data-sources/\"\u003eData Sources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 12\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Final project assignment.\u003c/li\u003e\n\u003cli\u003eLab: Hand out.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/assignments/\"\u003eAssignments\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 13\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Thanksgiving.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/\"\u003eResearch Resources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 14\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Activity 09 and Activity 10.\u003c/li\u003e\n\u003cli\u003eLab: Hand out.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/assignments/\"\u003eAssignments\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 15\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: BeagleTM.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/bioinformatics_resources/\"\u003eBioinformatics Resources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003eWeek 16\u003c/summary\u003e\n\u003cul\u003e\n\u003cli\u003eLecture: Course summary.\u003c/li\u003e\n\u003cli\u003ePresentations.\u003c/li\u003e\n\u003cli\u003eLearn more: \u003ca href=\"/resources/writing/\"\u003eWriting Resources\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\n\u003c/details\u003e\n\n"},{"title":"Search","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/search/","url":"https://computationalbioinformatics.com/search/","content_html":"\u003cp class=\"error message js-hidden\"\u003eYou must have Javascript enabled to use this function.\u003c/p\u003e\n\u003cp class=\"search-loading status message hidden\"\u003eLoading search index…\u003c/p\u003e\n\n\u003cdiv class=\"search-input hidden\"\u003e\n  \u003cform id=\"search-form\" class=\"search-form\" action=\"#\" method=\"post\" accept-charset=\"UTF-8\" role=\"search\"\u003e\n    \u003clabel for=\"query\" class=\"visually-hidden\"\u003eSearch\u003c/label\u003e\n    \u003cinput type=\"search\" id=\"query\" name=\"query\" class=\"search-text\" placeholder=\"Enter the terms you wish to search for.\" maxlength=\"128\"\u003e\n    \u003cbutton type=\"submit\" name=\"submit\" class=\"form-submit\" \u003eSearch\u003c/button\u003e\n  \u003c/form\u003e\n\u003c/div\u003e\n\n\u003cdiv class=\"search-results\"\u003e\u003c/div\u003e\n\n\u003ctemplate\u003e\n  \u003carticle class=\"search-result list-view\"\u003e\n    \u003cheader\u003e\n      \u003ch2 class=\"title title-submitted\"\u003e\u003ca href=\"#\"\u003eTitle here\u003c/a\u003e\u003c/h2\u003e\n      \u003cdiv class=\"submitted\"\u003e\u003ctime class=\"created-date\"\u003eDate here\u003c/time\u003e\u003c/div\u003e\n    \u003c/header\u003e\n    \u003cdiv class=\"content\"\u003eSummary here\u003c/div\u003e\n  \u003c/article\u003e\n\u003c/template\u003e\n\n"},{"title":"Tools and Environments","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/resources/tools-environments/","url":"https://computationalbioinformatics.com/resources/tools-environments/","content_html":"\u003ch1 id=\"tools-and-environments\" class=\"anchor-header\"\u003eTools and Environments \u003ca class=\"anchor-link\" href=\"#tools-and-environments\" aria-label=\"Tools and Environments\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h1\u003e\n\u003cp\u003eThis page describes a recommended setup for course work and a checklist for getting started.\u003c/p\u003e\n\u003ch2 id=\"recommended-software\" class=\"anchor-header\"\u003eRecommended software \u003ca class=\"anchor-link\" href=\"#recommended-software\" aria-label=\"Recommended software\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eMiniconda\u003c/strong\u003e or \u003cstrong\u003eMamba\u003c/strong\u003e for package management.\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://docs.conda.io/en/latest/miniconda.html\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://docs.conda.io/en/latest/miniconda.html\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://mamba.readthedocs.io/en/latest/installation.html\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://mamba.readthedocs.io/en/latest/installation.html\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003ePython 3.11+\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003eCore language for notebooks and scripting.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eJupyter\u003c/strong\u003e (Lab or Notebook)\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://jupyter.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://jupyter.org/\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eGit + GitHub\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://git-scm.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://git-scm.com/\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://github.com/\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eBLAST\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://blast.ncbi.nlm.nih.gov/Blast.cgi\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://blast.ncbi.nlm.nih.gov/Blast.cgi\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eBiopython\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://biopython.org/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003ehttps://biopython.org/\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"suggested-environment-checklist\" class=\"anchor-header\"\u003eSuggested environment checklist \u003ca class=\"anchor-link\" href=\"#suggested-environment-checklist\" aria-label=\"Suggested environment checklist\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003eInstall Python and a package manager.\u003c/li\u003e\n\u003cli\u003eCreate a new environment for this course.\u003c/li\u003e\n\u003cli\u003eInstall core libraries: \u003ccode\u003ebiopython\u003c/code\u003e, \u003ccode\u003epandas\u003c/code\u003e, \u003ccode\u003enumpy\u003c/code\u003e, \u003ccode\u003ematplotlib\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003eOpen a notebook and run a short test script.\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"example-conda-workflow\" class=\"anchor-header\"\u003eExample conda workflow \u003ca class=\"anchor-link\" href=\"#example-conda-workflow\" aria-label=\"Example conda workflow\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cdiv class=\"highlight\"\u003e\u003cpre tabindex=\"0\" style=\"color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;\"\u003e\u003ccode class=\"language-bash\" data-lang=\"bash\"\u003e\u003cspan style=\"display:flex;\"\u003e\u003cspan\u003econda create -n bioinfo python\u003cspan style=\"color:#f92672\"\u003e=\u003c/span\u003e3.11\n\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"display:flex;\"\u003e\u003cspan\u003econda activate bioinfo\n\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"display:flex;\"\u003e\u003cspan\u003econda install biopython pandas numpy matplotlib\n\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"display:flex;\"\u003e\u003cspan\u003epip install jupyterlab\n\u003c/span\u003e\u003c/span\u003e\u003c/code\u003e\u003c/pre\u003e\u003c/div\u003e\u003ch2 id=\"reproducibility-tips\" class=\"anchor-header\"\u003eReproducibility tips \u003ca class=\"anchor-link\" href=\"#reproducibility-tips\" aria-label=\"Reproducibility tips\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003eKeep environment files (e.g., \u003ccode\u003eenvironment.yml\u003c/code\u003e).\u003c/li\u003e\n\u003cli\u003eRecord software versions in reports.\u003c/li\u003e\n\u003cli\u003eUse clear file naming and folder structure.\u003c/li\u003e\n\u003c/ul\u003e\n\u003ch2 id=\"suggested-class-activity\" class=\"anchor-header\"\u003eSuggested class activity \u003ca class=\"anchor-link\" href=\"#suggested-class-activity\" aria-label=\"Suggested class activity\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h2\u003e\n\u003cul\u003e\n\u003cli\u003eSet up a new environment and run a short sequence parsing script.\u003c/li\u003e\n\u003c/ul\u003e\n"},{"title":"Writing Resources","date_published":"0001-01-01T00:00:00Z","date_modified":"0001-01-01T00:00:00Z","id":"https://computationalbioinformatics.com/resources/writing/","url":"https://computationalbioinformatics.com/resources/writing/","content_html":"\u003cp\u003e\u003cimg src=\"/resources/images/writerinspace.png\" alt=\"writer logo\"\u003e\u003c/p\u003e\n\u003ch4 id=\"how-can-i-write-better\" class=\"anchor-header\"\u003eHow can I write better? \u003ca class=\"anchor-link\" href=\"#how-can-i-write-better\" aria-label=\"How can I write better?\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cp\u003eWhen completing any assignment in research or in your classes, the quality of your writing is very important. Below are resources that may help you improve clarity, structure, and academic style.\u003c/p\u003e\n\u003chr\u003e\n\u003ch4 id=\"online-resources\" class=\"anchor-header\"\u003eOnline resources \u003ca class=\"anchor-link\" href=\"#online-resources\" aria-label=\"Online resources\"\u003e\n\u003csvg xmlns=\"http://www.w3.org/2000/svg\" class=\"anchor-icon\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" stroke-width=\"2\" stroke=\"currentColor\" fill=\"none\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\u003e\n  \u003cpath stroke=\"none\" d=\"M0 0h24v24H0z\" fill=\"none\"/\u003e\n  \u003cpath d=\"M10 14a3.5 3.5 0 0 0 5 0l4 -4a3.5 3.5 0 0 0 -5 -5l-.5 .5\" /\u003e\n  \u003cpath d=\"M14 10a3.5 3.5 0 0 0 -5 0l-4 4a3.5 3.5 0 0 0 5 5l.5 -.5\" /\u003e\n\u003c/svg\u003e\n\u003c/a\u003e\u003c/h4\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eMaytum Center for Student Success\u003c/strong\u003e: Writing and Speaking Consultants at Allegheny College\u0026rsquo;s \u003ca href=\"https://sites.allegheny.edu/studentsuccess/writing-speech/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eWriting Center\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003eUniversity of Maryland\u003c/strong\u003e: \u003ca href=\"https://www.umgc.edu/current-students/learning-resources/writing-center/online-guide-to-writing/tutorial/chapter4/ch4-06#:~:text=Research%20resources%20are%20found%20in,sources%20found%20on%20the%20Internet.\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eOnline Guide to Writing\u003c/a\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n"}]}