CINXE.COM
Bioconductor becomes a Carpentries member organization – Bioconductor community blog
<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head> <meta charset="utf-8"> <meta name="generator" content="quarto-1.6.40"> <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes"> <meta name="author" content="Charlotte Soneson"> <meta name="author" content="Laurent Gatto"> <meta name="author" content="Toby Hodges"> <meta name="author" content="Jenny Drnevich"> <meta name="author" content="Robert Castelo"> <meta name="author" content="Susan Holmes"> <meta name="dcterms.date" content="2022-07-12"> <meta name="description" content="Starting from August 1, 2022, Bioconductor will be a member of The Carpentries. Among other things, the membership enables us to allow 15 individuals to follow the Carpentries’ Instructor Training program and become certified Carpentries Instructors."> <title>Bioconductor becomes a Carpentries member organization – Bioconductor community blog</title> <style> code{white-space: pre-wrap;} span.smallcaps{font-variant: small-caps;} div.columns{display: flex; gap: min(4vw, 1.5em);} div.column{flex: auto; overflow-x: auto;} div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} ul.task-list{list-style: none;} ul.task-list li input[type="checkbox"] { width: 0.8em; margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ vertical-align: middle; } </style> <script src="../../site_libs/quarto-nav/quarto-nav.js"></script> <script src="../../site_libs/quarto-nav/headroom.min.js"></script> <script src="../../site_libs/clipboard/clipboard.min.js"></script> <script src="../../site_libs/quarto-search/autocomplete.umd.js"></script> <script src="../../site_libs/quarto-search/fuse.min.js"></script> <script src="../../site_libs/quarto-search/quarto-search.js"></script> <meta name="quarto:offset" content="../../"> <script src="../../site_libs/quarto-html/quarto.js"></script> <script src="../../site_libs/quarto-html/popper.min.js"></script> <script src="../../site_libs/quarto-html/tippy.umd.min.js"></script> <script src="../../site_libs/quarto-html/anchor.min.js"></script> <link href="../../site_libs/quarto-html/tippy.css" rel="stylesheet"> <link href="../../site_libs/quarto-html/quarto-syntax-highlighting-549806ee2085284f45b00abea8c6df48.css" rel="stylesheet" id="quarto-text-highlighting-styles"> <script src="../../site_libs/bootstrap/bootstrap.min.js"></script> <link href="../../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet"> <link href="../../site_libs/bootstrap/bootstrap-9c546a04fa00a275547e7eb78afa1c09.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light"> <script id="quarto-search-options" type="application/json">{ "location": "navbar", "copy-button": false, "collapse-after": 3, "panel-placement": "end", "type": "overlay", "limit": 50, "keyboard-shortcut": [ "f", "/", "s" ], "show-item-context": false, "language": { "search-no-results-text": "No results", "search-matching-documents-text": "matching documents", "search-copy-link-title": "Copy link to search", "search-hide-matches-text": "Hide additional matches", "search-more-match-text": "more match in this document", "search-more-matches-text": "more matches in this document", "search-clear-button-title": "Clear", "search-text-placeholder": "", "search-detached-cancel-button-title": "Cancel", "search-submit-button-title": "Submit", "search-label": "Search" } }</script> <script defer="" data-domain="bioconductor.github.io/biocblog" src="https://plausible.io/js/script.js"></script> <link rel="stylesheet" href="../../styles.css"> <meta property="og:title" content="Bioconductor becomes a Carpentries member organization – Bioconductor community blog"> <meta property="og:description" content="Starting from August 1, 2022, Bioconductor will be a member of The Carpentries. Among other things, the membership enables us to allow 15 individuals to follow the Carpentries’ Instructor Training program and become certified Carpentries Instructors."> <meta property="og:site_name" content="Bioconductor community blog"> </head> <body class="nav-fixed fullcontent"> <div id="quarto-search-results"></div> <header id="quarto-header" class="headroom fixed-top quarto-banner"> <nav class="navbar navbar-expand-lg " data-bs-theme="dark"> <div class="navbar-container container-fluid"> <div class="navbar-brand-container mx-auto"> <a class="navbar-brand" href="../../index.html"> <span class="navbar-title">Bioconductor community blog</span> </a> </div> <div id="quarto-search" class="" title="Search"></div> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }"> <span class="navbar-toggler-icon"></span> </button> <div class="collapse navbar-collapse" id="navbarCollapse"> <ul class="navbar-nav navbar-nav-scroll ms-auto"> <li class="nav-item"> <a class="nav-link" href="../../about.html"> <span class="menu-text">About</span></a> </li> <li class="nav-item"> <a class="nav-link" href="../../contributing.html"> <span class="menu-text">Contributing</span></a> </li> <li class="nav-item compact"> <a class="nav-link" href="https://github.com/bioconductor/biocblog"> <i class="bi bi-github" role="img"> </i> <span class="menu-text"></span></a> </li> <li class="nav-item compact"> <a class="nav-link" href="https://genomic.social/@bioconductor"> <i class="bi bi-mastodon" role="img"> </i> <span class="menu-text"></span></a> </li> <li class="nav-item compact"> <a class="nav-link" href="https://www.linkedin.com/company/bioconductor/"> <i class="bi bi-linkedin" role="img"> </i> <span class="menu-text"></span></a> </li> <li class="nav-item compact"> <a class="nav-link" href="https://www.youtube.com/user/bioconductor"> <i class="bi bi-youtube" role="img"> </i> <span class="menu-text"></span></a> </li> <li class="nav-item compact"> <a class="nav-link" href="https://slack.bioconductor.org/"> <i class="bi bi-slack" role="img"> </i> <span class="menu-text"></span></a> </li> <li class="nav-item compact"> <a class="nav-link" href="../../index.xml"> <i class="bi bi-rss" role="img"> </i> <span class="menu-text"></span></a> </li> </ul> </div> <!-- /navcollapse --> <div class="quarto-navbar-tools"> </div> </div> <!-- /container-fluid --> </nav> </header> <!-- content --> <header id="title-block-header" class="quarto-title-block default page-columns page-full"> <div class="quarto-title-banner page-columns page-full"> <div class="quarto-title column-body"> <h1 class="title">Bioconductor becomes a Carpentries member organization</h1> <div> <div class="description"> <p>Starting from August 1, 2022, Bioconductor will be a member of The Carpentries. Among other things, the membership enables us to allow 15 individuals to follow the Carpentries’ Instructor Training program and become certified Carpentries Instructors.</p> </div> </div> <div class="quarto-categories"> <div class="quarto-category">education</div> <div class="quarto-category">Carpentries</div> </div> </div> </div> <div class="quarto-title-meta"> <div> <div class="quarto-title-meta-heading">Authors</div> <div class="quarto-title-meta-contents"> <p><a href="http://csoneson.github.io/">Charlotte Soneson</a> </p> <p><a href="https://lgatto.github.io/">Laurent Gatto</a> </p> <p>Toby Hodges </p> <p>Jenny Drnevich </p> <p>Robert Castelo </p> <p>Susan Holmes </p> </div> </div> <div> <div class="quarto-title-meta-heading">Published</div> <div class="quarto-title-meta-contents"> <p class="date">July 12, 2022</p> </div> </div> </div> </header><div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar"> <!-- sidebar --> <!-- margin-sidebar --> <!-- main --> <main class="content quarto-banner-title-block" id="quarto-document-content"> <p>The <a href="https://bioconductor.org/help/education-training/">Bioconductor Teaching Committee</a> is happy to announce that starting from August 1, 2022 and <a href="https://chanzuckerberg.com/eoss/proposals/bioconductor-high-quality-training-and-support-for-a-worldwide-community/">supported by the Chan Zuckerberg Initiative</a>, Bioconductor will be a member of <a href="https://carpentries.org/">The Carpentries</a>, a global community of volunteers who develop and teach interactive, hands-on workshops on computing and data skills, addressing basic training needs that are unmet in most disciplines.</p> <p>Among other things, The Carpentries membership enables us to give 15 people from the Bioconductor community the opportunity to follow <a href="https://carpentries.org/become-instructor/">The Carpentries’ Instructor Training program</a> and become certified Carpentries Instructors. Certified Instructors can co-teach Carpentries workshops associated with Bioconductor events, and also have the opportunity to teach as part of a team at other institutions in The Carpentries network, meeting others with similar skills who enjoy sharing them. We would also encourage you to engage with the Bioconductor Teaching Committee and community in other ways, e.g. by participating in our monthly meetings and <a href="https://carpentries.org/blog/2021/07/incubator-lesson-spotlight-rna-seq-data-analysis/">contributing</a> to the Bioconductor-focused <a href="https://bioconductor.org/help/education-training/">training material</a> currently in development.</p> <p>The Carpentries Instructor Training is primarily focused on evidence-based teaching practices and does not include technical skills training. It is expected that trainees will have or will develop the technical skills necessary to guide learners through the entry level curricula for one or more Data Carpentry, Library Carpentry, or Software Carpentry workshops. Instructor Training is held remotely in either a 2-day, full day format or a 4-day, half-day format, and will be free-of-charge to selected Bioconductor community members.</p> <p>If you are interested in education and want to get involved in the Bioconductor teaching community as a certified Carpentries Instructor, please fill <a href="https://forms.gle/HvnhkZZkhEE54vqL9">this form</a> to express your interest. Suitable candidates will be selected on a rolling basis until all spots are filled and before January 2023. If you have questions, don’t hesitate to reach out to education@bioconductor.org.</p> <p> © 2025 Bioconductor. Content is published under <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons CC-BY-4.0 License</a> for the text and <a href="https://opensource.org/licenses/BSD-3-Clause">BSD 3-Clause License</a> for any code. | <a href="https://www.r-bloggers.com">R-Bloggers</a> </p></main> <!-- /main --> <script id="quarto-html-after-body" type="application/javascript"> window.document.addEventListener("DOMContentLoaded", function (event) { const toggleBodyColorMode = (bsSheetEl) => { const mode = bsSheetEl.getAttribute("data-mode"); const bodyEl = window.document.querySelector("body"); if (mode === "dark") { bodyEl.classList.add("quarto-dark"); bodyEl.classList.remove("quarto-light"); } else { bodyEl.classList.add("quarto-light"); bodyEl.classList.remove("quarto-dark"); } } const toggleBodyColorPrimary = () => { const bsSheetEl = window.document.querySelector("link#quarto-bootstrap"); if (bsSheetEl) { toggleBodyColorMode(bsSheetEl); } } toggleBodyColorPrimary(); const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { placement: 'right', icon: icon }; anchorJS.add('.anchored'); const isCodeAnnotation = (el) => { for (const clz of el.classList) { if (clz.startsWith('code-annotation-')) { return true; } } return false; } const onCopySuccess = function(e) { // button target const button = e.trigger; // don't keep focus button.blur(); // flash "checked" button.classList.add('code-copy-button-checked'); var currentTitle = button.getAttribute("title"); button.setAttribute("title", "Copied!"); let tooltip; if (window.bootstrap) { button.setAttribute("data-bs-toggle", "tooltip"); button.setAttribute("data-bs-placement", "left"); button.setAttribute("data-bs-title", "Copied!"); tooltip = new bootstrap.Tooltip(button, { trigger: "manual", customClass: "code-copy-button-tooltip", offset: [0, -8]}); tooltip.show(); } setTimeout(function() { if (tooltip) { tooltip.hide(); button.removeAttribute("data-bs-title"); button.removeAttribute("data-bs-toggle"); button.removeAttribute("data-bs-placement"); } button.setAttribute("title", currentTitle); button.classList.remove('code-copy-button-checked'); }, 1000); // clear code selection e.clearSelection(); } const getTextToCopy = function(trigger) { const codeEl = trigger.previousElementSibling.cloneNode(true); for (const childEl of codeEl.children) { if (isCodeAnnotation(childEl)) { childEl.remove(); } } return codeEl.innerText; } const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', { text: getTextToCopy }); clipboard.on('success', onCopySuccess); if (window.document.getElementById('quarto-embedded-source-code-modal')) { const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', { text: getTextToCopy, container: window.document.getElementById('quarto-embedded-source-code-modal') }); clipboardModal.on('success', onCopySuccess); } var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); var mailtoRegex = new RegExp(/^mailto:/); var filterRegex = new RegExp("https:\/\/blog\.bioconductor\.org\/"); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } // Inspect non-navigation links and adorn them if external var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)'); for (var i=0; i<links.length; i++) { const link = links[i]; if (!isInternal(link.href)) { // undo the damage that might have been done by quarto-nav.js in the case of // links that we want to consider external if (link.dataset.originalHref !== undefined) { link.href = link.dataset.originalHref; } } } function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) { const config = { allowHTML: true, maxWidth: 500, delay: 100, arrow: false, appendTo: function(el) { return el.parentElement; }, interactive: true, interactiveBorder: 10, theme: 'quarto', placement: 'bottom-start', }; if (contentFn) { config.content = contentFn; } if (onTriggerFn) { config.onTrigger = onTriggerFn; } if (onUntriggerFn) { config.onUntrigger = onUntriggerFn; } window.tippy(el, config); } const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]'); for (var i=0; i<noterefs.length; i++) { const ref = noterefs[i]; tippyHover(ref, function() { // use id or data attribute instead here let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href'); try { href = new URL(href).hash; } catch {} const id = href.replace(/^#\/?/, ""); const note = window.document.getElementById(id); if (note) { return note.innerHTML; } else { return ""; } }); } const xrefs = window.document.querySelectorAll('a.quarto-xref'); const processXRef = (id, note) => { // Strip column container classes const stripColumnClz = (el) => { el.classList.remove("page-full", "page-columns"); if (el.children) { for (const child of el.children) { stripColumnClz(child); } } } stripColumnClz(note) if (id === null || id.startsWith('sec-')) { // Special case sections, only their first couple elements const container = document.createElement("div"); if (note.children && note.children.length > 2) { container.appendChild(note.children[0].cloneNode(true)); for (let i = 1; i < note.children.length; i++) { const child = note.children[i]; if (child.tagName === "P" && child.innerText === "") { continue; } else { container.appendChild(child.cloneNode(true)); break; } } if (window.Quarto?.typesetMath) { window.Quarto.typesetMath(container); } return container.innerHTML } else { if (window.Quarto?.typesetMath) { window.Quarto.typesetMath(note); } return note.innerHTML; } } else { // Remove any anchor links if they are present const anchorLink = note.querySelector('a.anchorjs-link'); if (anchorLink) { anchorLink.remove(); } if (window.Quarto?.typesetMath) { window.Quarto.typesetMath(note); } if (note.classList.contains("callout")) { return note.outerHTML; } else { return note.innerHTML; } } } for (var i=0; i<xrefs.length; i++) { const xref = xrefs[i]; tippyHover(xref, undefined, function(instance) { instance.disable(); let url = xref.getAttribute('href'); let hash = undefined; if (url.startsWith('#')) { hash = url; } else { try { hash = new URL(url).hash; } catch {} } if (hash) { const id = hash.replace(/^#\/?/, ""); const note = window.document.getElementById(id); if (note !== null) { try { const html = processXRef(id, note.cloneNode(true)); instance.setContent(html); } finally { instance.enable(); instance.show(); } } else { // See if we can fetch this fetch(url.split('#')[0]) .then(res => res.text()) .then(html => { const parser = new DOMParser(); const htmlDoc = parser.parseFromString(html, "text/html"); const note = htmlDoc.getElementById(id); if (note !== null) { const html = processXRef(id, note); instance.setContent(html); } }).finally(() => { instance.enable(); instance.show(); }); } } else { // See if we can fetch a full url (with no hash to target) // This is a special case and we should probably do some content thinning / targeting fetch(url) .then(res => res.text()) .then(html => { const parser = new DOMParser(); const htmlDoc = parser.parseFromString(html, "text/html"); const note = htmlDoc.querySelector('main.content'); if (note !== null) { // This should only happen for chapter cross references // (since there is no id in the URL) // remove the first header if (note.children.length > 0 && note.children[0].tagName === "HEADER") { note.children[0].remove(); } const html = processXRef(null, note); instance.setContent(html); } }).finally(() => { instance.enable(); instance.show(); }); } }, function(instance) { }); } let selectedAnnoteEl; const selectorForAnnotation = ( cell, annotation) => { let cellAttr = 'data-code-cell="' + cell + '"'; let lineAttr = 'data-code-annotation="' + annotation + '"'; const selector = 'span[' + cellAttr + '][' + lineAttr + ']'; return selector; } const selectCodeLines = (annoteEl) => { const doc = window.document; const targetCell = annoteEl.getAttribute("data-target-cell"); const targetAnnotation = annoteEl.getAttribute("data-target-annotation"); const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation)); const lines = annoteSpan.getAttribute("data-code-lines").split(","); const lineIds = lines.map((line) => { return targetCell + "-" + line; }) let top = null; let height = null; let parent = null; if (lineIds.length > 0) { //compute the position of the single el (top and bottom and make a div) const el = window.document.getElementById(lineIds[0]); top = el.offsetTop; height = el.offsetHeight; parent = el.parentElement.parentElement; if (lineIds.length > 1) { const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]); const bottom = lastEl.offsetTop + lastEl.offsetHeight; height = bottom - top; } if (top !== null && height !== null && parent !== null) { // cook up a div (if necessary) and position it let div = window.document.getElementById("code-annotation-line-highlight"); if (div === null) { div = window.document.createElement("div"); div.setAttribute("id", "code-annotation-line-highlight"); div.style.position = 'absolute'; parent.appendChild(div); } div.style.top = top - 2 + "px"; div.style.height = height + 4 + "px"; div.style.left = 0; let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter"); if (gutterDiv === null) { gutterDiv = window.document.createElement("div"); gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter"); gutterDiv.style.position = 'absolute'; const codeCell = window.document.getElementById(targetCell); const gutter = codeCell.querySelector('.code-annotation-gutter'); gutter.appendChild(gutterDiv); } gutterDiv.style.top = top - 2 + "px"; gutterDiv.style.height = height + 4 + "px"; } selectedAnnoteEl = annoteEl; } }; const unselectCodeLines = () => { const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"]; elementsIds.forEach((elId) => { const div = window.document.getElementById(elId); if (div) { div.remove(); } }); selectedAnnoteEl = undefined; }; // Handle positioning of the toggle window.addEventListener( "resize", throttle(() => { elRect = undefined; if (selectedAnnoteEl) { selectCodeLines(selectedAnnoteEl); } }, 10) ); function throttle(fn, ms) { let throttle = false; let timer; return (...args) => { if(!throttle) { // first call gets through fn.apply(this, args); throttle = true; } else { // all the others get throttled if(timer) clearTimeout(timer); // cancel #2 timer = setTimeout(() => { fn.apply(this, args); timer = throttle = false; }, ms); } }; } // Attach click handler to the DT const annoteDls = window.document.querySelectorAll('dt[data-target-cell]'); for (const annoteDlNode of annoteDls) { annoteDlNode.addEventListener('click', (event) => { const clickedEl = event.target; if (clickedEl !== selectedAnnoteEl) { unselectCodeLines(); const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active'); if (activeEl) { activeEl.classList.remove('code-annotation-active'); } selectCodeLines(clickedEl); clickedEl.classList.add('code-annotation-active'); } else { // Unselect the line unselectCodeLines(); clickedEl.classList.remove('code-annotation-active'); } }); } const findCites = (el) => { const parentEl = el.parentElement; if (parentEl) { const cites = parentEl.dataset.cites; if (cites) { return { el, cites: cites.split(' ') }; } else { return findCites(el.parentElement) } } else { return undefined; } }; var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]'); for (var i=0; i<bibliorefs.length; i++) { const ref = bibliorefs[i]; const citeInfo = findCites(ref); if (citeInfo) { tippyHover(citeInfo.el, function() { var popup = window.document.createElement('div'); citeInfo.cites.forEach(function(cite) { var citeDiv = window.document.createElement('div'); citeDiv.classList.add('hanging-indent'); citeDiv.classList.add('csl-entry'); var biblioDiv = window.document.getElementById('ref-' + cite); if (biblioDiv) { citeDiv.innerHTML = biblioDiv.innerHTML; } popup.appendChild(citeDiv); }); return popup.innerHTML; }); } } }); </script> </div> <!-- /content --> </body></html>