{"version":"https://jsonfeed.org/version/1.1","title":"Research Resources on Computational Bioinformatics","description":"Recent content in Research Resources on Computational Bioinformatics","home_page_url":"https://computationalbioinformatics.com/","feed_url":"https://computationalbioinformatics.com/resources/index.json","language":"en-GB","favicon":"https://computationalbioinformatics.com/logo.png","authors":[{"name":"Oliver Bonham-Carter","url":"https://oliverbonhamcarter.com"}],"items":[{"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":"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"}]}