{"id":746,"date":"2020-10-21T11:00:17","date_gmt":"2020-10-21T09:00:17","guid":{"rendered":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/?page_id=746"},"modified":"2024-03-21T09:12:01","modified_gmt":"2024-03-21T07:12:01","slug":"getting-started","status":"publish","type":"page","link":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/?page_id=746","title":{"rendered":"Getting started in the lab"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"746\" class=\"elementor elementor-746\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-d4b4e8a elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"d4b4e8a\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-a4db5be\" data-id=\"a4db5be\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-3a96b89 elementor-widget elementor-widget-heading\" data-id=\"3a96b89\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Welcome to the lab!<\/h2>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-28c38ae5 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"28c38ae5\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-6cd672e1\" data-id=\"6cd672e1\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-13a92661 elementor-widget elementor-widget-text-editor\" data-id=\"13a92661\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<p><span style=\"font-size: 1rem;\">We&#8217;re happy to have you here! In the lab we use a set of tools to&nbsp;<\/span>streamline<span style=\"font-size: 1rem;\">&nbsp;our work and collaborate. In order to help you get started, here are the main programs.<\/span><\/p>\n<ul>\n<li>We communicate using&nbsp;<strong>Keybase<\/strong>. We have a lab calendar on google calendar.<\/li>\n<li>Programming:\n<ul>\n<li>We usually program in <strong>R<\/strong>, using RStudio. We also use <b>Python<\/b> and <b>Julia<\/b>.<\/li>\n<li>We use&nbsp;<strong>GitHub<\/strong> for version control and collaborating on code.<\/li>\n<li>We use Markdown, specifically&nbsp;<strong>R notebooks<\/strong> to document our code, analysis, and results, all in one file.<\/li>\n<\/ul>\n<\/li>\n<li>We read papers and manage our references using&nbsp;<strong>Paperpile<\/strong>.<\/li>\n<li>We writre papers in <b>Latex<\/b>.<\/li>\n<\/ul>\n<h2>Lab toolbox<\/h2>\n<div>We have created a <a href=\"https:\/\/github.com\/Ecological-Complexity-Lab\/lab_toolbox\">GitHub repository with examples of the computational tools we use<\/a>.<\/div>\n<h2>Creating Accounts:<\/h2>\n<p><span style=\"font-weight: 400;\">Keybase, GitHub, Paperpile, and Google docs and Calendar all require accounts, and the lab has groups\/repositories\/etc in each that you need to be invited to. <\/span><span style=\"font-weight: 400;\">Using your BGU account is recommended.<\/span><\/p>\n<h2>Program and Application Details and Tutorials:<\/h2>\n<h4><b>Keybase:<\/b><\/h4>\n<p><span style=\"font-weight: 400;\"><a href=\"https:\/\/keybase.io\/\">Keybase<\/a> has direct messages and channels for different topics. <\/span><span style=\"font-weight: 400;\">Use it to chat with lab members&nbsp;<\/span><span style=\"color: var( --e-global-color-text ); font-family: var( --e-global-typography-text-font-family ), Sans-serif; font-size: 1rem;\">or to post questions, files, code or whatever you need in the relevant channels. You need an invitation to join our team.<\/span><\/p>\n<h4><b>GitHub:<\/b><\/h4>\n<p><span style=\"font-weight: 400;\"><a href=\"https:\/\/github.com\/\">GitHub<\/a> is a platform for code version control and collaboration, it stores the code in a shared place, and provides version control. See <a href=\"https:\/\/guides.github.com\/\">here<\/a> <\/span><span style=\"font-weight: 400;\">for a tutorial. Also there is a short exercise to get you started&nbsp;<\/span><a href=\"https:\/\/github.com\/Ecological-Complexity-Lab\/data_science_tutorials\" target=\"_blank\" rel=\"noopener\">here<\/a>.<span style=\"font-weight: 400;\">&nbsp; To use GitHub open a student account, which should be a PRO account and ask Geut\/Shirly to add you to our&nbsp;<\/span><a href=\"https:\/\/github.com\/Ecological-Complexity-Lab\" target=\"_blank\" rel=\"noopener\">lab&#8217;s GitHub organization<\/a><span style=\"font-weight: 400;\">.<\/span><\/p>\n<h4><b>R:<\/b><\/h4>\n<p><span style=\"font-weight: 400;\">Our lab\u2019s primary programming language! <a href=\"https:\/\/datacarpentry.org\/R-ecology-lesson\/\/00-before-we-start.html\">Here<\/a> <\/span><span style=\"font-weight: 400;\">is a great place to get started with both R and RStudio. <a href=\"https:\/\/www.statmethods.net\/r-tutorial\/index.html\">Here<\/a> <\/span><span style=\"font-weight: 400;\">is another useful tutorial, and there are plenty of others online. We mainly use R because this is the common language among ecologists. You are welcome to use other languages if you need.<\/span><\/p>\n<h4><b>R notebooks:<\/b><\/h4>\n<p><span style=\"font-weight: 400;\">These are files that allow you to keep code, code results, analyses, text, tables, graphs, etc in one elegant, readable, and reprogrammable file. When generating the polished file it runs the code contained in it, allowing it to create results internally, no need to copy an image into the file and lose image quality. R notebooks are a specific type of R Markdown file. You can start <a href=\"https:\/\/rmarkdown.rstudio.com\/\">here<\/a>, <\/span><span style=\"font-weight: 400;\">and once you have a GitHub account and permission to access our lab\u2019s repositories, you can also use <a href=\"https:\/\/github.com\/Ecological-Complexity-Lab\/data_science_tutorials\">this<\/a>.<\/span><\/p>\n<h4><b>Paperpile:<\/b><\/h4>\n<p><span style=\"font-weight: 400;\"><a href=\"https:\/\/paperpile.com\">Paperpile<\/a> helps you manage papers for your research, and is an excellent tool for managing references. There is a Paperpile chrome extension for Google docs. Please open an account, you can start with the 1 month free trial until you have a paid account via the lab. They have a guide to help get you started <a href=\"https:\/\/paperpile.com\/h\/guide-paperpile-web-app\/\">here<\/a><\/span><span style=\"font-weight: 400;\">.<\/span><\/p>\n<h4><b>Lab&#8217;s virtual library:<\/b><\/h4>\n<p>There is a collection of books that you will find very useful for learning networks, analysis with R and theory. All concentrated in&nbsp;<a href=\"https:\/\/paperpile.com\/shared\/qJq6aw\" target=\"_blank\" rel=\"noopener\">our virtual library<\/a>. Just download the PDFs.<\/p>\n<h4><b>Google docs:<\/b><\/h4>\n<p><span style=\"font-weight: 400;\">You can use the Google Drive and Google Docs that you have in your post.bgu account. We have a team drive to throw in files and write-ups.<\/span><\/p>\n<h4><b>Google Calendar:<\/b><\/h4>\n<p>In order to more easily sync events between lab members, and keep everyone informed of future lab meetings and events we use Google Calendar. You will join our lab calendar<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Welcome to the lab! We&#8217;re happy to have you here! In the lab we use a set of tools to&nbsp;streamline&nbsp;our work and collaborate. In order to help you get started, here are the main programs. We communicate using&nbsp;Keybase. We have a lab calendar on google calendar. Programming: We usually program in R, using RStudio. We &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/?page_id=746\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Getting started in the lab&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-746","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=\/wp\/v2\/pages\/746","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=746"}],"version-history":[{"count":28,"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=\/wp\/v2\/pages\/746\/revisions"}],"predecessor-version":[{"id":2427,"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=\/wp\/v2\/pages\/746\/revisions\/2427"}],"wp:attachment":[{"href":"https:\/\/lifewp.bgu.ac.il\/wp\/pilos\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=746"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}