{"id":61252,"date":"2022-11-24T09:36:42","date_gmt":"2022-11-24T09:36:42","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/?post_type=vf_event&#038;p=61252"},"modified":"2022-11-24T09:36:45","modified_gmt":"2022-11-24T09:36:45","slug":"swc19-01","status":"publish","type":"vf_event","link":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/events\/swc19-01\/","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-53de8397-0f08-449c-b4a4-0fdca47249f2\" data-vf-js-location-nearest-activation-target=\"\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-311a4dae-4712-45c4-bb7c-83f569003b70\" data-vf-js-location-nearest-activation-target=\"\">Speakers<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-88113a31-4a51-4c85-a47e-d124b3842495\" data-vf-js-location-nearest-activation-target=\"\">Programme<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-53de8397-0f08-449c-b4a4-0fdca47249f2\"><h2 class=\"vf-u-sr-only\">Overview<\/h2>\n<h2 class=\"wp-block-heading\">Course Overview<\/h2>\n\n\n\n<p>Computation is an integral part of today&#8217;s research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. 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 using inefficient tools when progress could be faster. 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<h2 class=\"wp-block-heading\">Audience<\/h2>\n\n\n\n<p>This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line\/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git).<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Modules\/Resources<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li>Introduction to Python scripting<\/li><li>Introduction to the Unix shell and usage of cluster resources<\/li><li>Version control with Git and Github<\/li><li>Analysis pipeline management<\/li><li>Scientific Python &amp; working with biological data<\/li><li>Literate programming with Jupyter notebooks<\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Learning Outcomes<\/h2>\n\n\n\n<p>After the workshop, participants will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>write and organise their own scripts for data analysis<\/li><li>use version control to keep track of, and revert changes to their files<\/li><li>implement&nbsp;efficient and reproducible pipelines that combine multiple tools and scripts&nbsp;<\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-311a4dae-4712-45c4-bb7c-83f569003b70\"><h2 class=\"vf-u-sr-only\">Speakers<\/h2>\n<h2 class=\"wp-block-heading\">Speakers and Trainers<\/h2>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Alves_Renato.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Renato Alves            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Dinkel_Holger.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Holger Dinkel            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Max Planck Institute for Biological Cybernetics            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Hodges_Toby1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Toby Hodges            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Schwarzl_Thomas.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Thomas Schwarzl            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Sharan_Malvika1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Malvika Sharan            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Thommen_Frank.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Frank Thommen            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                DKFZ Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                 Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Scientific Organisers<\/h2>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Hodges_Toby1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Toby Hodges            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                 Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Sharan_Malvika1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Malvika Sharan            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Zeller_Georg.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Georg Zeller            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\">\n<h2 class=\"wp-block-heading\">Course Organisers<\/h2>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n            <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/dev.assets.emblstatic.net\/vf\/v2.0.0-alpha.6\/assets\/vf-summary\/assets\/vf-icon--avatar.svg\" > \n    \n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Maria Mercedes Bacadare Goitia            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n<\/div><\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-88113a31-4a51-4c85-a47e-d124b3842495\"><h2>Programme<\/h2>\n<p id=\"block-1984fb46-4b9e-4350-bb7b-3decc4627750\"><\/p>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-543be599-c9c1-479a-a993-46311484afc3\" href=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/EMBL-Course-Computing-Skills-For-Reproducible-Research_-Software-Carpentry-Programme.pdf\">EMBL-Course-Computing-Skills-For-Reproducible-Research_-Software-Carpentry-Programme<\/a><\/div>\n\n\n\n<p><\/p>\n<\/section>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\"><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"parent":0,"menu_order":0,"template":"","embl_taxonomy":[],"class_list":["post-61252","vf_event","type-vf_event","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"vf_event_start_date":{"value":"20191016","formatted":"16 October 2019"},"vf_event_end_date":{"value":"20191018","formatted":"18 October 2019"},"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":"","formatted":""},"vf_event_additional_info":{"value":"","formatted":""},"vf_event_registration_fee":{"value":"","formatted":""},"vf_event_canceled":{"value":"no","formatted":"no"},"vf_event_venue":{"value":"","formatted":""},"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\/swc19-01\/","formatted":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/events\/swc19-01\/"},"vf_event_registration_link":{"value":"mailto: ","formatted":"mailto: "},"vf_event_start_time":{"value":"","formatted":""},"vf_event_end_time":{"value":"","formatted":""},"vf_event_location":{"value":["67"],"formatted":["EMBL Heidelberg"]},"vf_event_time_zone":{"value":"europe\/berlin","formatted":"Europe\/Berlin"},"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":"","formatted":""},"vf_event_displayed":{"value":"EMBL Course","formatted":"EMBL 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