{"id":20,"date":"2024-04-04T04:36:11","date_gmt":"2024-04-04T01:36:11","guid":{"rendered":"https:\/\/sisu.ut.ee\/andmehaldus\/open-source-code\/"},"modified":"2024-04-16T18:03:23","modified_gmt":"2024-04-16T15:03:23","slug":"open-source-code","status":"publish","type":"page","link":"https:\/\/sisu.ut.ee\/andmehaldus\/open-source-code\/?lang=en","title":{"rendered":"Open Source Code"},"content":{"rendered":"<p style=\"text-align: justify\">\n\tPractising of Open Science requires the using of open source code software for data processing, which is licenced in the way that everyone can use, edit and improve it.\n<\/p>\n<p style=\"text-align: justify\">\n\tIt is reasonable to use the already acknowledged universal software. However, occasionally it may be necessary to write some original code for solving some certain problems.\n<\/p>\n<p style=\"text-align: justify\">\n\tOpen source code should be treated just like any other research data or methods, it is important to pay attention to documenting the software and workflow, to metadata, to version control and licences.\u00a0\u00a0\n<\/p>\n<blockquote>\n<p style=\"text-align: justify\">\n\t\tIn order to make research results transparent and reproducible, the accompanying software has to allow repetition of all the analyses done in the course of research.\n\t<\/p>\n<\/blockquote>\n<p style=\"text-align: justify\">\n\tIt is advisable to use the version control system <a data-url=\"https:\/\/git-scm.com\/\" href=\"https:\/\/git-scm.com\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Git<\/a> and\u00a0the\u00a0cloud-based code repositories like\u00a0<a data-url=\"https:\/\/github.com\/\" href=\"https:\/\/github.com\/\" target=\"_blank\" title=\"\" rel=\"noopener\">GitHub<\/a>,\u00a0<a data-url=\"https:\/\/about.gitlab.com\/\" href=\"https:\/\/about.gitlab.com\/\" target=\"_blank\" title=\"\" rel=\"noopener\">GitLab<\/a>\u00a0(when using <a data-url=\"https:\/\/gitlab.ut.ee\/users\/sign_in\" href=\"https:\/\/gitlab.ut.ee\/users\/sign_in\" target=\"_blank\" title=\"\" rel=\"noopener\">UT credentials<\/a>\u00a0choose\u00a0<em>Sign in with Sibboleth<\/em>), <a data-url=\"https:\/\/bitbucket.org\/product\" href=\"https:\/\/bitbucket.org\/product\" target=\"_blank\" title=\"\" rel=\"noopener\">Bitbucket<\/a>\u00a0etc.\n<\/p>\n<p style=\"text-align: justify\">\n\tIt is said that software can never be completed. Therefore, it is necessary to think about whether you will be able to offer user support to your code in the future.\n<\/p>\n<p style=\"text-align: justify\">\n\tThe article <em><a data-url=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1005412.s001\" href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1005412.s001\" target=\"_blank\" title=\"\" rel=\"noopener\">Ten simple rules for making research software more robust<\/a><\/em>\u00a0contains a <a data-url=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/research_software_checklist.pdf\" href=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/research_software_checklist.pdf\" target=\"_blank\" title=\"\" rel=\"noopener\">checklist<\/a> for software developers.\n<\/p>\n<p style=\"text-align: center\">\n\t<img decoding=\"async\" alt=\"tenrules\" src=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/software_ten_rules.png\" style=\"width: 613px;height: 416px\">\n<\/p>\n<p style=\"text-align: justify\">\n\tUseful recommendations about version control can be found in the article\u00a0<a data-url=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1007142\" href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1007142\" target=\"_blank\" title=\"\" rel=\"noopener\"><em>Ten Simple Rules for Taking Advantage of Git and GitHub<\/em><\/a>\n<\/p>\n<p style=\"text-align: justify\">\n\t<a href=\"https:\/\/d1rkab7tlqy5f1.cloudfront.net\/Websections\/ICT%20Innovation\/TU%20Delft%20OSS%20Guidelines_draft%201.0.pd\" target=\"_blank\" rel=\"noopener\">A guide<\/a> has been developed at Delft University about how to licence software created for research or open education. The added diagram helps to decide how to proceed.\n<\/p>\n<p style=\"text-align: center\">\n\t<img decoding=\"async\" alt=\"\" src=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/os_software.png\" style=\"width: 613px;height: 594px\">\n<\/p>\n<p style=\"text-align: center\">\n\t<a href=\"https:\/\/www.tudelft.nl\/en\/ict-innovation\/articles\/open-source-software-guidelines-for-researchers\" target=\"_blank\" rel=\"noopener\">Resource<\/a>\n<\/p>\n<p style=\"text-align: justify\">\n\tChoose a licence for open source code:\u00a0<a data-url=\"https:\/\/choosealicense.com\/\" href=\"https:\/\/choosealicense.com\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Choose a Licence<\/a>.\n<\/p>\n<p style=\"text-align: justify\">\n\tSome good advice from software engineer Peter Kalverla:\u00a0\n<\/p>\n<p style=\"text-align: justify\">\n\t<\/p><div class=\"ratio ratio-16x9 mb-3\"><div class=\"video-placeholder-wrapper video-placeholder-wrapper--16x9\">\n\t\t\t    <div class=\"video-placeholder d-flex justify-content-center align-items-center\">\n\t\t\t        <div class=\"overlay text-white p-2 w-100 text-center d-block justify-content-center align-items-center\">\n\t\t\t            <div>Kolmandate osapoolte sisu n\u00e4gemiseks palun n\u00f5ustu k\u00fcpsistega.<\/div>\n\t\t\t            <button class=\"btn btn-secondary btn-sm mt-1 consent-change\">Muuda n\u00f5usolekut<\/button>\n\t\t\t        <\/div>\n\t\t\t    <\/div>\n\t\t\t<\/div>\n<\/div>\n\n<p style=\"text-align: justify\">\n\t\u00a0\n<\/p>\n<p>\n\tOn selge, et ettevalmistused oma tarkvara jagamiseks ja teiste koodi m\u00f5istmine ning kasutamine ei ole lihtne.\u00a0<br>Allj\u00e4rgnevas k\u00fcsitlusuuringus oli 188 vastajat ning huvitav on uurida, kui paljud tunnevad huvi teadusartikliga seotud koodi vastu ning kui ajamahukas on ettevalmistus selle avaldamiseks:\u00a0\n<\/p>\n<p>\n\tIt is quite obvious that prepering the code for sharing and understanding other peoples\u2019 code is not easy. There is a survey with 188 respondents discussing these matters from the point of view of researcher publishing an article.\u00a0\n<\/p>\n<p>\n\tCadwallader L, Hrynaszkiewicz I.\u00a02022.\u00a0<strong>A survey of researchers\u2019 code sharing and code reuse practices, and assessment of interactive notebook prototypes<\/strong>.\u00a0PeerJ\u00a010:e13933\u00a0<a href=\"https:\/\/doi.org\/10.7717\/peerj.13933\">https:\/\/doi.org\/10.7717\/peerj.13933<\/a>\n<\/p>\n<p style=\"text-align: center\">\n\t<img loading=\"lazy\" decoding=\"async\" width=\"623\" height=\"487\" class=\"alignnone wp-image-123\" src=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/koodihuvilised.png\" title=\"koodihuvilised.png\" alt=\"koodihuvilised\" srcset=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/koodihuvilised.png 623w, https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/koodihuvilised-300x235.png 300w\" sizes=\"auto, (max-width: 623px) 100vw, 623px\">\n<\/p>\n<p style=\"text-align: center\">\n\t<img loading=\"lazy\" decoding=\"async\" width=\"621\" height=\"419\" class=\"alignnone wp-image-124\" src=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/koodiaeg.png\" title=\"koodiaeg.png\" alt=\"koodiaeg\" srcset=\"https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/koodiaeg.png 621w, https:\/\/sisu.ut.ee\/wp-content\/uploads\/sites\/301\/koodiaeg-300x202.png 300w\" sizes=\"auto, (max-width: 621px) 100vw, 621px\">\n<\/p>\n<p>\n\tThere is a booklet published in France,\u00a0<a data-url=\"https:\/\/www.ouvrirlascience.fr\/source-code-and-software\/\" href=\"https:\/\/www.ouvrirlascience.fr\/source-code-and-software\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Open Science \u2013 Source code and software<\/a>, which goes through the following topics:\u00a0\u00a0What legal status do source code and software have? Why and how should we make them open access? How best to structure their\u00a0 development and ensure permanent archiving? How should we\u00a0 approach promotion?\n<\/p>\n<p style=\"text-align: justify\">\n\t\u00a0<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Practising of Open Science requires the using of open source code software for data processing, which is licenced in the way that everyone can use, edit and improve it. It is reasonable to use the already acknowledged universal software. However, &#8230;<\/p>\n","protected":false},"author":78,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"class_list":["post-20","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/pages\/20","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/users\/78"}],"replies":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/comments?post=20"}],"version-history":[{"count":1,"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/pages\/20\/revisions"}],"predecessor-version":[{"id":344,"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/pages\/20\/revisions\/344"}],"wp:attachment":[{"href":"https:\/\/sisu.ut.ee\/andmehaldus\/wp-json\/wp\/v2\/media?parent=20"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}