{"id":35938,"date":"2024-04-08T12:11:24","date_gmt":"2024-04-08T16:11:24","guid":{"rendered":"https:\/\/web.uri.edu\/riinbre\/?p=35938"},"modified":"2026-04-07T16:48:48","modified_gmt":"2026-04-07T20:48:48","slug":"introduction-to-biological-data-science_wdt2024","status":"publish","type":"post","link":"https:\/\/web.uri.edu\/riinbre\/introduction-to-biological-data-science_wdt2024\/","title":{"rendered":"WDT 2024 – Biological Data Science"},"content":{"rendered":"

Introduction to Biological Data Analysis<\/h1>\n

Instructors: Christopher Hemme, PhD, University of Rhode Island and Jillian Wise, PhD, Salve Regina University<\/h2>\n

Location: URI <\/strong> <\/em> 
\nSession 1: June 23-25 ( Location 205 Avedisian Hall)
\nSession 2: July 14-16 ( Location 205 Avedisian Hall)<\/p>\n

Course Overview<\/h3>\n

This WDT Module aims to train students in basic methods of biological data science.  It will cover concepts in using the Unix command line in a high-performance computing environment, introduction to the R programming language, design of biomedical experiments, and basic statistical analyses (e.g. t-test, ANOVA, regression).  Finally, students will get a basic introduction to bioinformatics and omics methods.<\/span> The module will be completed over 2.5 days and participants who complete the module will receive an RI-INBRE Certificate of completion.<\/p>\n

Learning Outcomes<\/h2>\n
    \n
  • Learn how to use the Unix command line on URI\u2019s Unity High-Performance Computing Cluster<\/span><\/li>\n
  • Learn basic concepts in biomedical experimental design, such as selection of controls, determining proper sample sizes, and different experimental setups<\/span><\/li>\n
  • Process different types of biomedical data using common statistical concepts such as <\/span>t<\/span><\/i>-test, ANOVA, and linear regression<\/span><\/li>\n
  • Learn basic concepts in bioinformatics including omics data analysis<\/span><\/li>\n
  • Analyze bioinformatics data using established methods such as differential expression analysis<\/span><\/li>\n<\/ul>\n

    Lab Report<\/h2>\n

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

      \n
    • Data analysis protocols (e.g., workflows, software used, etc.)<\/li>\n
    • Quality control metrics for sequencing and data analysis<\/li>\n
    • Results of data analysis<\/span><\/li>\n<\/ul>\n

      Resources Used in this Module:<\/h2>\n
        \n
      • Jupyter Notebooks for Hands-On Bioinformatics Data Analysis<\/li>\n
      • Slide Decks for Lectures<\/li>\n<\/ul>\n

        Proposed Timeline (subject to change)<\/h2>\n\n\n\n\n\t\n\n\t\n\t\n\t\n\t\n\t\n\t\n\t
        <\/td>Day 1<\/th>Day 2<\/th>Day 3<\/th>\n<\/tr>\n<\/thead>\n
        9:00 AM-10:00 AM<\/td>Introduction to Best Practices in Biomedical Data Science (Lecture)<\/td>Experimental Design and Power Analysis for Determining Sample Size for Biomedical Experiments (Lecture and Hands-On)<\/td>Single Cell Identification (Hands-On)<\/td>\n<\/tr>\n
        10:00 AM-11:00 AM<\/td>Using the Unix Command Line and Interactive Tools (Jupyter Notebooks and RStudio) on High-Performance Computing Clusters (Hands-On)<\/td>Methods for Exploratory Analysis of Biomedical Data (Lecture and Hands-On)<\/td>Exploratory Analysis of Single Cell Data (Hands-On)<\/td>\n<\/tr>\n
        11:00 AM-12:00 PM<\/td>R Programming I \u2013 Basic Data Structures and Functions (Hands-On)<\/td>Statistical Methods for Analysis of Biomedical Data (ANOVA, t-Test, linear regression, logistic regression) (Lecture\/Hands-On)<\/td>Artificial Intelligence in Biomedical Data Analysis (Optional, if time allows)<\/td>\n<\/tr>\n
        12:00 - 1:00 PM<\/td>Break<\/td>Break<\/td>WDT Survey and
        \nCertificate Distribution<\/td>\n<\/tr>\n
        1:00 PM-2:00 PM<\/td>R Programming II \u2013 Tidy Data and Tidyverse (Hands On)<\/td>Introduction to Bioinformatics and Single Cell Omics (Lecture)<\/td><\/td>\n<\/tr>\n
        2:00 PM-3:00 PM<\/td>R Programming III \u2013 Data Visualization (Hands On)<\/td>Processing of Single Cell Data (Hands-On)<\/td><\/td>\n<\/tr>\n
        3:00 PM-4:00 PM<\/td>Basic Statistical Concepts for Biomedical Research <\/td>Processing of Single Cell Data Cont. (Hands-On)<\/td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n","protected":false},"excerpt":{"rendered":"

        Introduction to Biological Data Analysis Instructors: Christopher Hemme, PhD, University of Rhode Island and Jillian Wise, PhD, Salve Regina University Location: URI    Session 1: June 23-25 ( Location 205 Avedisian Hall) Session 2: July 14-16 ( Location 205 Avedisian Hall) Course Overview This WDT Module aims to train students in basic methods of biological […]<\/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-35938","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"acf":[],"_links":{"self":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/35938","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=35938"}],"version-history":[{"count":5,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/35938\/revisions"}],"predecessor-version":[{"id":37959,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/posts\/35938\/revisions\/37959"}],"wp:attachment":[{"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/media?parent=35938"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/categories?post=35938"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.uri.edu\/riinbre\/wp-json\/wp\/v2\/tags?post=35938"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}