{"id":2286,"date":"2026-04-13T09:53:00","date_gmt":"2026-04-13T08:53:00","guid":{"rendered":"https:\/\/web.unibas.it\/parente\/?p=2286"},"modified":"2026-04-13T10:40:59","modified_gmt":"2026-04-13T09:40:59","slug":"making-the-most-of-foodmicrobionet","status":"publish","type":"post","link":"https:\/\/web.unibas.it\/parente\/?p=2286","title":{"rendered":"Making the most of FoodMicrobionet &#8211; a webinar"},"content":{"rendered":"\n<p>It is almost time for the webinar, which will take place on Tuesday, April 21st, 2026 15:00 CET (this is to allow people from the USA and Alberta to attend without having to wake up before sunrise&#8230;). A few things worth knowing:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>you can find FoodMicrobionet and related scripts in my <a href=\"https:\/\/github.com\/ep142\/FoodMicrobionet\">GitHub repository<\/a>. You may want to check out how to <a href=\"https:\/\/docs.github.com\/en\/repositories\/creating-and-managing-repositories\/cloning-a-repository\">clone a repository<\/a>, and <a href=\"https:\/\/docs.github.com\/en\/get-started\/start-your-journey\/downloading-files-from-github\">how to download a folder or a raw file<\/a>.<\/li>\n\n\n\n<li>you can find a downloadable version of the ShinyFMBN app on <a href=\"https:\/\/data.mendeley.com\/datasets\/8fwwjpm79y\/13\" data-type=\"link\" data-id=\"https:\/\/data.mendeley.com\/datasets\/8fwwjpm79y\/13\">Mendeley data<\/a> and on <a href=\"https:\/\/github.com\/ep142\/FoodMicrobionet\/tree\/master\/shiny_apps\/shiny_FMBN_4_light\" data-type=\"link\" data-id=\"https:\/\/github.com\/ep142\/FoodMicrobionet\/tree\/master\/shiny_apps\/shiny_FMBN_4_light\">GitHub<\/a>: you are strongly encouraged to download the app because running it locally is much faster<\/li>\n\n\n\n<li>you can run the app on Shinyapps.io by clicking on <a href=\"https:\/\/ep142.shinyapps.io\/ShinyFMBN_4_light\/\">this link<\/a> <\/li>\n\n\n\n<li>further resources (studies with ASVs) are available on <a href=\"https:\/\/zenodo.org\/records\/18590893\" data-type=\"link\" data-id=\"https:\/\/zenodo.org\/records\/18590893\">Zenodo<\/a><\/li>\n\n\n\n<li>I will make available more example scripts next week so check the GitHub repository just before the webinar for the most recent version of the scripts<\/li>\n<\/ul>\n\n\n\n<p>If you are one of the few people left in the world who still reads manuals:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Table specifications for FoodMicrobionet are <a href=\"https:\/\/github.com\/ep142\/FoodMicrobionet\/blob\/master\/the_real_thing\/FMBN_5_1\/FMBN_5_1_2_tablespecs\/FMBN5_1_tablespecs_v_1_0.md\">here<\/a><\/li>\n\n\n\n<li>Instruction manual for the ShinyFMBN app are <a href=\"https:\/\/github.com\/ep142\/FoodMicrobionet\/blob\/master\/shiny_apps\/shiny_FMBN_4_light\/ShinyFMBNManual_v4_gh.md\">here<\/a><\/li>\n<\/ul>\n\n\n\n<p><strong>Please note<\/strong>: I will be accepting people in the webinar (you should be logged in the browser with the address you have used for registering) in the first 15 minutes<\/p>\n\n\n\n<p>The following scientific papers are related to FoodMicrobionet<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Parente, E., Cocolin, L., Filippis, F.D., Zotta, T., Ferrocino, I., O\u2019Sullivan, O., Neviani, E., Angelis, M.D., Cotter, P.D., Ercolini, D., 2016. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis. International Journal of Food Microbiology 219, 28\u201337. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2015.12.001<\/li>\n\n\n\n<li>Parente, E., Filippis, F.D., Ercolini, D., Ricciardi, A., Zotta, T., 2019. Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database. International Journal of Food Microbiology 305, 108249. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2019.108249<\/li>\n\n\n\n<li>Parente, E., Ricciardi, A., Zotta, T., 2020. The microbiota of dairy milk: A review. Int Dairy J 107, 104714. https:\/\/doi.org\/10.1016\/j.idairyj.2020.104714<\/li>\n\n\n\n<li>Parente, E., Zotta, T., Ricciardi, A., 2021. Microbial association networks in cheese: a meta-analysis. Biorxiv 2021.07.21.453196. https:\/\/doi.org\/10.1101\/2021.07.21.453196<\/li>\n\n\n\n<li>Zotta, T., Ricciardi, A., Condelli, N., Parente, E., 2022. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Crit Rev Food Sci 62, 3898\u20133912. https:\/\/doi.org\/10.1080\/10408398.2020.1870927<\/li>\n\n\n\n<li>Parente, E., Zotta, T., Ricciardi, A., 2022. A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 368, 109618. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2022.109618<\/li>\n\n\n\n<li>Parente, E., Zotta, T., Ricciardi, A., 2022. FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities. Int. J. Food Microbiol. 372, 109696. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2022.109696<\/li>\n\n\n\n<li>Parente, E., Zotta, T., Giavalisco, M., Ricciardi, A., 2023. Metataxonomic insights in the distribution of <em>Lactobacillaceae<\/em> in foods and food environments. Int J Food Microbiol 391, 110124. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2023.110124<\/li>\n\n\n\n<li>Parente, E., Ricciardi, A., 2024. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 13, 1689. https:\/\/doi.org\/10.3390\/foods13111689<\/li>\n\n\n\n<li>Ricciardi, A., L\u00f3pez, F.N.A., Giavalisco, M., Pietrafesa, R., Parente, E., 2025. Determining the core bacterial and fungal genera in table olive fermentations. Int. J. Food Microbiol. 442, 111344. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2025.111344<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>It is almost time for the webinar, which will take place on Tuesday, April 21st, 2026 15:00 CET (this is to allow people from the USA and Alberta to attend without having to wake up before sunrise&#8230;). A few things &hellip; <a href=\"https:\/\/web.unibas.it\/parente\/?p=2286\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[23,54,1],"tags":[],"class_list":["post-2286","post","type-post","status-publish","format-standard","hentry","category-foodmicrobionet","category-ncydiversity","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/posts\/2286","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2286"}],"version-history":[{"count":6,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/posts\/2286\/revisions"}],"predecessor-version":[{"id":2293,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=\/wp\/v2\/posts\/2286\/revisions\/2293"}],"wp:attachment":[{"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2286"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2286"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.unibas.it\/parente\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2286"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}