{"id":64093,"date":"2025-08-12T14:38:57","date_gmt":"2025-08-12T14:38:57","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/data-science-centre\/?page_id=64093"},"modified":"2026-03-11T13:31:43","modified_gmt":"2026-03-11T13:31:43","slug":"scientific-workflows","status":"publish","type":"page","link":"https:\/\/www.embl.org\/about\/info\/data-science-centre\/scientific-workflows\/","title":{"rendered":"Scientific Workflows"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\"><strong>About Scientific Workflows<\/strong><\/h2>\n\n\n\n<p>Scientific workflows are structured, automated pipelines used to process, analyze, and manage complex data sets. Tools like Snakemake and Nextflow provide frameworks for defining these workflows in a reproducible, scalable, and portable manner.&nbsp; They make it easier to integrate multiple software tools and help simplify the process of scaling your analysis from running locally on your laptop to the EMBL high-performance computing cluster.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>How can Scientific Workflows help your research?<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Reproducibility<\/strong>: Ensure consistent results by automating analysis steps and recording all parameters, software versions, and input files.<\/li>\n\n\n\n<li><strong>Scalability<\/strong>: Efficiently process large data sets by parallelizing tasks across multiple CPUs or the HPC cluster.<\/li>\n\n\n\n<li><strong>Transparency<\/strong>: Clarify complex analyses by making each step of the data processing pipeline explicit and easy to review.<\/li>\n\n\n\n<li><strong>Efficiency<\/strong>: Save time and reduce errors through automation, minimizing manual intervention and repetitive tasks.<\/li>\n\n\n\n<li><strong>Collaboration<\/strong>: Share workflows with collaborators or the broader scientific community, enhancing knowledge transfer and method dissemination.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Our Services<\/strong><\/h2>\n\n\n\n<p>We offer consultation services to help EMBL researchers design, implement, and maintain scientific workflows using tools like Snakemake and Nextflow. Whether you&#8217;re starting from scratch or looking to improve existing pipelines, we provide:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Topic introductions for those interested in using workflow management systems.<\/li>\n\n\n\n<li>Workflow design and development support, from simple scripts to complex, multi-step pipelines.<\/li>\n\n\n\n<li>Assistance with integrating workflows into the EMBL HPC cluster.<\/li>\n\n\n\n<li>Troubleshooting and optimization of existing workflows to improve performance and reproducibility.<\/li>\n\n\n\n<li>Documentation and best-practices guidance to ensure long-term maintainability.<\/li>\n<\/ul>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/s.embl.org\/datascience-consulting\">\n      Request a consultation       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n                <p class=\"vf-card__text\">Provide details about your project, and we&#8217;ll match you with the most suitable consultant to schedule a session.<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<h2 class=\"wp-block-heading\">Contact<\/h2>\n\n\n<div class=\"vf-content-hub-html\" data-cache=\"3875f130\">\n      <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=person&amp;filter-field-contains%5Bfield_person_embl_id%5D=CP-60034623&amp;filter-fields-empty=field_person_visible_internally&amp;filter-ref-entity%5Bfield_person_positions%5D%5Btitle%5D=&amp;filter-ref-entity%5Bfield_person_positions%5D%5Bfield_position_primary%5D=1&amp;hide%5Bteam%2Cemail%2Corcid%5D=1&amp;limit=1&amp;pattern=vf-profile-inline -->\n                \n                            <article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline\" data-embl-js-conditional-edit=\"87622\">\n              <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/content.embl.org\/\/sites\/default\/files\/styles\/medium\/public\/persons\/CP-60034623.jpg?itok=v-f-IreS\" alt=\"image of Francesco Tabaro\" \/>\n      \n              <h3 class=\"vf-profile__title\">\n                      <a href=\"https:\/\/www.embl.org\/people\/person\/francesco-tabaro\" class=\"vf-profile__link\">Francesco Tabaro<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-profile__job-title\">\n          Genomics Data Platform Developer\n        <\/p>\n      \n      \n      \n      \n      \n      \n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/87622\/87622\" target=\"_blank\">\n        Edit\n      <\/a>\n    <\/article>\n  <\/div>\n\n\n<div class=\"vf-content-hub-html\" data-cache=\"d2da2fa9\">\n      <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=person&amp;filter-field-contains%5Bfield_person_embl_id%5D=CP-60044184&amp;filter-fields-empty=field_person_visible_internally&amp;filter-ref-entity%5Bfield_person_positions%5D%5Btitle%5D=&amp;filter-ref-entity%5Bfield_person_positions%5D%5Bfield_position_primary%5D=1&amp;hide%5Bteam%2Cemail%2Cphones%2Corcid%5D=1&amp;limit=1&amp;pattern=vf-profile-inline -->\n                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class=\"vf-content-hub-html\" data-cache=\"be9f2870\">\n      <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=person&amp;filter-field-contains%5Bfield_person_embl_id%5D=CP-60100500&amp;filter-fields-empty=field_person_visible_internally&amp;filter-ref-entity%5Bfield_person_positions%5D%5Btitle%5D=&amp;filter-ref-entity%5Bfield_person_positions%5D%5Bfield_position_primary%5D=1&amp;hide%5Bteam%2Cemail%2Cphones%2Corcid%5D=1&amp;limit=1&amp;pattern=vf-profile-inline -->\n                \n                            <article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline\" data-embl-js-conditional-edit=\"560403\">\n              <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/content.embl.org\/\/sites\/default\/files\/styles\/medium\/public\/persons\/CP-60100500.jpg?itok=PQgVMvmw\" alt=\"image of Erick Martins Ratamero\" \/>\n      \n              <h3 class=\"vf-profile__title\">\n                      <a href=\"https:\/\/www.embl.org\/people\/person\/erick-martinsratamero\" class=\"vf-profile__link\">Erick Martins Ratamero<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-profile__job-title\">\n          Data Management Coordinator\n        <\/p>\n      \n      \n      \n      \n      \n      \n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/560403\/560403\" target=\"_blank\">\n        Edit\n      <\/a>\n    <\/article>\n  <\/div>\n\n\n<div class=\"vf-content-hub-html\" data-cache=\"31562f7f\">\n      <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=person&amp;filter-field-contains%5Bfield_person_full_name%5D=vivanco&amp;filter-fields-empty=field_person_visible_internally&amp;filter-ref-entity%5Bfield_person_positions%5D%5Btitle%5D=&amp;filter-ref-entity%5Bfield_person_positions%5D%5Bfield_position_primary%5D=1&amp;hide%5Bteam%2Cemail%2Cphones%2Corcid%5D=1&amp;limit=1&amp;pattern=vf-profile-inline -->\n                \n                      <article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline\" data-embl-js-conditional-edit=\"1443285\">\n              <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/assets.emblstatic.net\/vf\/v2.4.14\/assets\/vf-summary\/assets\/vf-icon--avatar.svg\" alt=\"image of Nora Vivanco Gonzalez\" \/>\n      \n              <h3 class=\"vf-profile__title\">\n                      <a href=\"https:\/\/www.embl.org\/people\/person\/nora-vivanco-gonzalez\" class=\"vf-profile__link\">Nora Vivanco Gonzalez<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-profile__job-title\">\n          Data Scientist for Imaging and Omics\n        <\/p>\n      \n      \n      \n      \n      \n      \n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/1443285\/1443285\" target=\"_blank\">\n        Edit\n      <\/a>\n    <\/article>\n  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