{"id":277461,"date":"2026-07-16T13:52:39","date_gmt":"2026-07-16T12:52:39","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/?post_type=vf_event&#038;p=277461"},"modified":"2026-10-20T09:41:45","modified_gmt":"2026-10-20T08:41:45","slug":"swc27-01","status":"publish","type":"vf_event","link":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/events\/swc27-01\/","title":{"rendered":"Computing skills for reproducible research: software carpentry"},"content":{"rendered":"\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-overview\" data-vf-js-location-nearest-activation-target=\"\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-sponsors\" data-vf-js-location-nearest-activation-target=\"\">Sponsors<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-media-kit\" data-vf-js-location-nearest-activation-target=\"\">Media kit<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-overview\"><h2 class=\"vf-u-sr-only\">Overview<\/h2>\n<p class=\"wp-block-paragraph\">Applications for this event are not open yet. If you are interested in receiving more information, please register your interest.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Course overview<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">As data has grown too large or too complex to analyse by hand, computation has become integral to today\u2019s research. An ever-growing fraction of science is performed computationally, but many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent doing steps manually or using inefficient tools when progress could be faster.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Modules\/resources<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Introduction to the Unix shell<\/li>\n\n\n\n<li>Version control and history tracking with Git<\/li>\n\n\n\n<li>Introduction to scripting and basics of data analysis with Python<\/li>\n\n\n\n<li>Introduction to reproducible computational research with Nextflow<\/li>\n\n\n\n<li>Introduction to Large Language Models (LLMs) for coding<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Audience<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">This course is aimed at researchers in the life sciences who wish to use analysis pipelines on individual computers or clusters of computers. The target learner is familiar with some command line\/programmatic computer usage, and wants to become more confident using these tools efficiently and reproducibly.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">If you have written a for-loop in some language before, but do not know your way around the command line, or if you\u2019ve committed a file to Git, but don\u2019t know how to restore it, you may be the perfect fit for this workshop.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Learning outcomes<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">After the course, participants will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Interact with a command-line shell for local and remote computing needs<\/li>\n\n\n\n<li>write and organise their own scripts for data analysis<\/li>\n\n\n\n<li>Use version control to keep track of, and revert changes to their files<\/li>\n\n\n\n<li>Run efficient and reproducible pipelines that combine multiple tools and scripts<\/li>\n\n\n\n<li>Understand how coding agents may assist them in their data analysis tasks and the associated risks<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">What past participants say about the course<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><em>\u201cI highly recommend the Software Carpentry course, as it covers all the necessary basics, and by the end of the week you are able to write your own little program for your own purposes.\u201d<\/em>&nbsp;\u2013 Erzsebet Baka, Department of Molecular Ecology, Hungarian University of Agriculture and Life Sciences, Hungary<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><em>\u201cAn excellent course with excellent and very nice mentors who are always willing to help. The organization is fantastic, and they help you with any questions you may have.\u201d<\/em>\u00a0\u2014 William Zamora, University of Costa Rica, Costa Rica<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-sponsors\"><h2>Sponsors<\/h2>\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Sponsorship opportunities<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget.&nbsp;Discounts are available for companies sponsoring multiple events at EMBL Heidelberg.&nbsp;<a href=\"http:\/\/www.embl.de\/training\/events\/index.php?p_eventType=CON&amp;amp;p_outstation=HD&amp;amp;p_timeRange=FUTURE&amp;amp;submit=Show+Events\">View other conferences<\/a>, or contact&nbsp;<a href=\"mailto:sponsorship@embl.de\">sponsorship@embl.de<\/a>&nbsp;for further information.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">If you are interested in becoming a media partner of this event, please visit our&nbsp;<a href=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/sponsor-an-event\/#vf-tabs__section-08208670-4ad4-45ca-a4ff-ac6edb6ffd0b\" target=\"_blank\" rel=\"noreferrer noopener\">media partnerships webpage<\/a>.<\/p>\n\n\n\n<div class=\"wp-block-buttons is-layout-flex wp-block-buttons-is-layout-flex\"><p><a href=\"mailto:sponsorship@embl-em.de?subject=%20Request%20a%20Sponsorship%20Brochure&#038;body=Please%20kindly%20send%20me%20the%20sponsorship%20brochure%20for%20(please%20indicate%20the%20event%20your%20are%20interested%20in).\" class=\"vf-button vf-button--primary vf-button--pill\">Request a sponsorship brochure<\/a><\/p><\/div>\n\n\n\n<div class=\"vf-box vf-box--normal vf-box-theme--quaternary | vf-u-margin__bottom--400\">\n      <h3 class=\"vf-box__heading\">\n                Warning                  <\/h3> \n        <p class=\"vf-box__text\">EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name \u2018Judy Eastman\u2019 (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL\u2019s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.<\/p>\n<p class=\"vf-box__text\">Please also note that:<\/p>\n<ul>\n<li><span style=\"font-size: 12pt\">EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.<\/span><\/li>\n<li><span style=\"font-size: 12pt\">EMBL will never call or email you to ask for your credit card details or to request a payment.<\/span><\/li>\n<li><span style=\"font-size: 12pt\">All payments are on invoice.<\/span><\/li>\n<\/ul>\n<p class=\"vf-box__text\">Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsoring@embl.de.<\/p>\n<\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-media-kit\"><h2>Media kit<\/h2>\n<p class=\"wp-block-paragraph\">Want to let others know you&#8217;re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.<\/p>\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-centered  size-large is-resized\"><a href=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_stories_MK.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"576\" height=\"1024\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_stories_MK-576x1024.jpg\" alt=\"\" class=\"wp-image-284497\" style=\"width:169px;height:auto\" srcset=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_stories_MK-576x1024.jpg 576w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_stories_MK-169x300.jpg 169w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_stories_MK-768x1365.jpg 768w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_stories_MK-864x1536.jpg 864w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_stories_MK.jpg 1080w\" sizes=\"auto, (max-width: 576px) 100vw, 576px\" \/><\/a><figcaption class=\"vf-figure__caption\">Social 1080&#215;1920<\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image size-large is-resized is-style-default\"><a href=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_ig_media_kit.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"819\" height=\"1024\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_ig_media_kit-819x1024.jpg\" alt=\"\" class=\"wp-image-284501\" style=\"width:256px;height:auto\" srcset=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_ig_media_kit-819x1024.jpg 819w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_ig_media_kit-240x300.jpg 240w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_ig_media_kit-768x960.jpg 768w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_ig_media_kit.jpg 1080w\" sizes=\"auto, (max-width: 819px) 100vw, 819px\" \/><\/a><figcaption class=\"vf-figure__caption\">Social 1080&#215;1350<\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image size-medium is-resized\"><a href=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01-FB.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"300\" height=\"169\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01-FB-300x169.jpg\" alt=\"\" class=\"wp-image-284503\" style=\"width:300px;height:auto\" srcset=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01-FB-300x169.jpg 300w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01-FB-1024x576.jpg 1024w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01-FB-768x432.jpg 768w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01-FB-1536x864.jpg 1536w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01-FB.jpg 1600w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a><figcaption class=\"vf-figure__caption\">Social 1600&#215;900<\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-centered  size-medium\"><a href=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_STD.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"300\" height=\"169\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_STD-300x169.jpg\" alt=\"\" class=\"wp-image-284495\" srcset=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_STD-300x169.jpg 300w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_STD-1024x576.jpg 1024w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_STD-768x432.jpg 768w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_STD-1536x864.jpg 1536w, https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_STD.jpg 1920w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a><\/figure>\n\n\n\n<p class=\"vf-text--body vf-text-body--3 wp-block-paragraph\">PPT Slide 16&#215;9<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n<\/div><\/div>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"parent":0,"menu_order":0,"template":"","embl_taxonomy":[],"class_list":["post-277461","vf_event","type-vf_event","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"vf_event_start_date":{"value":"20270719","formatted":"19 July 2027"},"vf_event_end_date":{"value":"20270723","formatted":"23 July 2027"},"vf_event_submission_opening":{"value":"","formatted":""},"vf_event_submission_closing":{"value":"","formatted":""},"vf_event_registration_opening":{"value":"","formatted":""},"vf_event_registration_closing":{"value":"","formatted":""},"vf_event_summary":{"value":"<span data-sheets-root=\"1\">This hands-on workshop teaches researchers the fundamental skills they need to reproducibly conduct and scale their computational work, providing high-quality, domain-specific training covering use and customisation of new or existing data analysis pipelines.<\/span>","formatted":"<p><span data-sheets-root=\"1\">This hands-on workshop teaches researchers the fundamental skills they need to reproducibly conduct and scale their computational work, providing high-quality, domain-specific training covering use and customisation of new or existing data analysis pipelines.<\/span><\/p>\n"},"vf_event_additional_info":{"value":"","formatted":""},"vf_event_registration_fee":{"value":"","formatted":""},"vf_event_canceled":{"value":"no","formatted":"no"},"vf_event_venue":{"value":"EMBL Advanced Training Centre, EMBL Rome","formatted":"EMBL Advanced Training Centre, EMBL Rome"},"vf_event_unique_identifier":{"value":"","formatted":""},"vf_event_event_type":{"value":"course","formatted":{"value":"course","label":"Course"}},"vf_event_more_information_link":{"value":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/events\/swc27-01\/","formatted":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/events\/swc27-01\/"},"vf_event_registration_link":{"value":"","formatted":""},"vf_event_start_time":{"value":"","formatted":""},"vf_event_end_time":{"value":"","formatted":""},"vf_event_location":{"value":["67","69"],"formatted":["EMBL Heidelberg","EMBL Rome"]},"vf_event_time_zone":{"value":"europe\/london","formatted":"Europe\/London"},"vf_event_ss_subtype":{"value":null,"formatted":null},"vf_event_embo_subtype":{"value":"","formatted":""},"vf_event_featured":{"value":"0","formatted":false},"vf_event_organisers_listing":{"value":"Christian Schudoma, Deborah Udoh, Francesco Tabaro, Lisanna  Paladin, Renato 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12:49:52","menu_order":0,"mime_type":"image\/jpeg","type":"image","subtype":"jpeg","icon":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-includes\/images\/media\/default.png","width":2083,"height":2083,"sizes":{"thumbnail":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_SCREENS-150x150.jpg","thumbnail-width":150,"thumbnail-height":150,"medium":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_SCREENS-300x300.jpg","medium-width":300,"medium-height":300,"medium_large":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_SCREENS-768x768.jpg","medium_large-width":768,"medium_large-height":768,"large":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_SCREENS-1024x1024.jpg","large-width":1024,"large-height":1024,"1536x1536":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_SCREENS-1536x1536.jpg","1536x1536-width":1536,"1536x1536-height":1536,"2048x2048":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_SCREENS-2048x2048.jpg","2048x2048-width":2048,"2048x2048-height":2048,"vf-hero":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/SWC27-01_SCREENS.jpg","vf-hero-width":2083,"vf-hero-height":2083}}},"vf_event_custom_overview":{"value":"Computation is an integral part of today\u2019s research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally but many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. This course is aimed at researchers in the life sciences who wish to use or design analysis pipelines on individual or clusters of computers.","formatted":"Computation is an integral part of today\u2019s research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally but many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. 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