{"id":35985,"date":"2024-04-09T11:50:31","date_gmt":"2024-04-09T15:50:31","guid":{"rendered":"https:\/\/web.uri.edu\/riinbre\/?p=35985"},"modified":"2026-04-03T13:19:40","modified_gmt":"2026-04-03T17:19:40","slug":"3d-science-visualization_wdt2024","status":"publish","type":"post","link":"https:\/\/web.uri.edu\/riinbre\/3d-science-visualization_wdt2024\/","title":{"rendered":"WDT 2026 3D Science Visualization"},"content":{"rendered":"

3D Science Visualization<\/h1>\n

Instructor: Bongsup Cho, PhD, University of Rhode Island<\/h2>\n

Location: URI <\/strong> <\/em> 
Session 1: June 29-July 1 (Avedisian Hall Room 205)
Session 2: July 13-15 (Avedisian Hall Room 205)<\/p>\n

Course Overview<\/h3>\n

This WDT Module aims to train students in modern methods of 3D science visualization. The module will include lectures and hands-on experience in molecular modeling, 3D molecule printing, protein and DNA structure prediction using the AI-based machine learning algorithm AlphaFold, Tour of Human Cell, membrabe trasporters, and the BioRender Science Illustration app. The module will provide sufficient background for students to understand and appreciate how scientists could benefit from the available state-of-the-art 3D visualization software and tools to enhance their scientific data and disseminate it with impact. The module will be completed over 2.5 days, and participants who complete it will receive an RI-INBRE Certificate of Completion.<\/p>\n

 <\/p>\n

Learning Outcomes<\/h3>\n
    \n
  • \n
      \n
    • Navigate molecular structure databases such as the RCSB Protein Data Bank (PDB): Opioid Receptor as an example (4dkl)<\/li>\n
    • Visualize the molecular mechanisms of RNA-based antibiotics and cancer drugs using modeling<\/li>\n
    • Get hands-on with processing molecular structures in visualization software such as ChimeraX<\/li>\n
    • 3D-Print your molecular models<\/li>\n
    • Explore DNA structures and hands-on modeling of the origin of double helical structures<\/li>\n
    • Tour of Human Cell and demo<\/li>\n
    • Closer inspection of phospholipid transmembrane-bound ion channels and their structures and functions (Aquaporin, K+ Channel, and Na+ Channel)<\/li>\n
    • Hands-on practice on predicting protein structures from sequence using the Nobel prize-winning machine learning algorithm AlphaFold (Chris Hemme)
      \n
        \n
      • Demo of \u201cBioRender\u201d Scientific Image and Illustration Visualization Software (Chris Hemme)<\/li>\n
      • Reflection on scientists\/artists\u2019 interdisciplinary collaboration<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n

        Lab Report<\/h3>\n

        Students will be expected to maintain detailed laboratory notes to include:<\/p>\n

          \n
        • Structures analyzed and their relevance<\/li>\n
        • 3D printing protocols, inspection of macromolecules<\/li>\n
        • Data analysis protocols (e.g., workflows, software used, etc.)<\/li>\n
        • Results of AlphaFold analysis<\/li>\n<\/ul>\n

          Resources Used in this Module:<\/h3>\n
            \n
          • Standard Operating Procedure \u2013 3D Printing of Protein Structures<\/li>\n
          • ChimeraX \u2013 3D structure visualization of PDB files<\/li>\n
          • Slide Decks for lectures<\/li>\n
          • BioRender Image and Illustration Software<\/li>\n
          • \u201c3D Molecular Designs\u201d Kits (DNA, Ion Channels, Phospholipid membrane models)<\/li>\n
          • Illustration of a Human Cell<\/li>\n<\/ul>\n

            Proposed Timeline (subject to change)<\/h3>\n

             <\/p>\n\n\n

            D<\/td>Day 1<\/td>Day 2<\/td>Day 3<\/td><\/tr>
            9:00 AM – 10:00 AM<\/td>Introduction to Molecular Visualization and Structural Databases (Lecture)<\/td>Protein structures prediction using AlphaFold (Lecture\/Hands-on)<\/td><\/td><\/tr>
            10:00 AM – 11:00 AM<\/td>Tour of Model Showcase
            Tour of a Human Cell<\/td>            		Protein structures prediction using AlphaFold (Hands-on)<\/td>3D Printing Chimera (continues)<\/td><\/tr>
            11:00 AM – 12:00 PM<\/td>Antiobiotics action and resistance (Hands-on)<\/td>Demo of BioRender (Scientific image and illustration software)<\/td>Reflections<\/td><\/tr>
            12:00 PM – 1:00 PM<\/td>Break<\/td>Break<\/td>Certificate Distribution<\/td><\/tr>
            1:00 PM – 2:00 PM<\/td>3D Projection of drug actions (Hands-on)<\/td>Let’s play. Modeling of DNA structures and the origin of double helical structures (Hands-on)<\/td><\/td><\/tr>
            2:00 PM – 3:00 PM<\/td>ChimeraX Prep of 3D molecule printing (Hands-on)<\/td>DNA structure…continues. Modeling of phospholipid transmembrane (Hands-on)<\/td><\/td><\/tr>
            3:00 PM – 4:00 PM<\/td>ChimeraX Prep of 3D molecule printing (Hands-on)<\/td>DNA structure…continues. Modeling of phospholipid transmembrane (Hands-on)<\/td><\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"

            3D Science Visualization Instructor: Bongsup Cho, PhD, University of Rhode Island Location: URI   Session 1: June 29-July 1 (Avedisian Hall Room 205)Session 2: July 13-15 (Avedisian Hall Room 205) Course Overview This WDT Module aims to train students in modern methods of 3D science visualization. The module will include lectures and hands-on experience in molecular […]<\/p>\n","protected":false},"author":3192,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-35985","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"acf":[],"_links":{"self":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/35985","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/users\/3192"}],"replies":[{"embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/comments?post=35985"}],"version-history":[{"count":4,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/35985\/revisions"}],"predecessor-version":[{"id":37935,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/35985\/revisions\/37935"}],"wp:attachment":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/media?parent=35985"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/categories?post=35985"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/tags?post=35985"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}