Course Catalog

This class will provide an overview of Bioconductor. We will learn how to identify Bioconductor packages that are appropriate for a project, explore package documentation, and demonstrate how to download and install R packages from Bioconductor. 

Upon completion of this class participants should be able to describe what the Bioconductor project comprises, navigate the Bioconductor website to find packages for a particular task, install and update Bioconductor package, open a package vignette and practice running through the examples that they contain, and ensure that they are using the correct version of R to work with packages.

Camtasia is an all-in-one screen recording and editing software suite used to create video tutorials and presentations. In this introductory class, participants will learn how to use this tool to record their screen, add narration, video effects, transitions, and more. The class also provides an overview of basic controls and features available in Camtasia, during which participants will gain skills to produce a video from beginning to end.

This class will explore the basic functions and best practices for searching in Embase. The class will provide an overview of using the quick, advanced, PICO, PV Wizard, Medical Device and Drug search options. In addition, it will cover the Emtree searching taxonomy, saving search results, and setting up alerts. Attendees should come prepared with a basic search topic to actively search in Embase throughout the session. 

This class is recommended for novice searchers and pairs well with other database-specific classes, like Introduction to PubMed, Introduction to Web of Science, and more.   

EndNote 20 is a reference management tool that tracks citations and formats them as you write your manuscript. This introductory session covers how to: download the latest version of EndNote from the NIH Library; import records into EndNote; create, manage, and share EndNote libraries; and insert formatted citations into a Word document using the "Cite While You Write" feature.

EndNote Desktop provides access to EndNote records allowing the user to collect and organize references and insert them into a manuscript. This introductory session provides hands-on learning including importing records into EndNote, creating, managing, and sharing EndNote libraries, and inserting formatted citations into a Word document using the “Cite While You Write” feature.

PubMed comprises tens of millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. This hands-on introductory class will provide a journey into this valuable resource providing participants with an overview of its content, tools, and features. The session will cover steps to conduct a search, access full-text articles, and export results to a bibliographic management software such as EndNote.

This class is designed for those who want to extend the basics of R Markdown and apply those skills in Quarto. Quarto is an open-source scientific and technical publishing system that offers multilingual programming language support to create dynamic and static documents, books, presentations, blogs, and other online resources.

In this class you will learn about the similarities and differences between R-markdown and Quarto. You will also learn how to use Quarto to render documents in multiple formats, with a focus on scholarly publishing. Upon completion of this class participants will be able to distinguish between R-markdown and Quarto, identify publishing workflows using markdown, demonstrate the differences between the visual and source editors, create basic markdown elements, learn how to create and run code-blocks, and render a markdown document in multiple formats.

This is the first class in the NIH Library Introduction to R Series. This class provides a basic overview of the functionality of R programming language and RStudio. R is a programming language and open source environment for statistical computing and graphics. The R class series is a comprehensive collection of training sessions offered by the NIH Library Data Services and Bioinformatics programs that is designed to teach non-programmers how to write modular code and to introduce best practices for using R for data analysis and data visualization. Each class uses both evidence-based best practices for programming and practical hands-on lessons.

By the end of this class, students should be able to: list reasons for using R; describe the purpose of the RStudio Script, Console, Environment, and Plots panes; describe the various methods for finding help on R and RStudio; organize files and directories for a set of analyses as an R Project; define the following terms as they relate to R: object, assign, comment, call, function, and arguments; and assign values to objects in R.

Students are encouraged to install R and RStudio before the class so that they can follow along with the instructor. Please bring your laptop with R and RStudio installed.

During the COVID-19 pandemic, the number of rapid reviews increased and became a popular method of conducting a rigorous literature review, using systematic review methodology in a shorter time frame. This type of review helps synthesize the available evidence in a narrative descriptive format and can be done at a faster pace than a full systematic review. The introductory class will discuss what research questions are best suited for a rapid review, best practices for their conduct, and review the required methodological steps on how to conduct an effective rapid review. 

A scoping review is a preliminary assessment of research literature that aims to systematically map the literature, clarify concepts, and identify the evidence and knowledge gaps on a topic. This research method can be conducted as standalone review or used as an initial step before conducting a full systematic review. Participants will learn best practices, tips, and guidelines on how to conduct a scoping review. This introductory class will also include scoping review resources and an overview of NIH Library research support services.

Scopus is a comprehensive abstract and citation database that includes tens of millions of records from journals, books, and conference proceedings. It contains hundreds of thousands of books and peer-reviewed articles, and millions of conference papers. This introductory session will provide a hands-on tutorial providing participants with skills to search for publications, conduct author and affiliation searches, create alerts, view citation counts and export results to a bibliographic management software such as EndNote.

The BTRIS Limited Data Set application allows researchers to access data from across all active and terminated protocols conducted within the NIH intramural program. Access clinical research data from 1976 to the present across more than a half million subjects to pose hypotheses and generate new research ideas.

Class Prerequisites:
You must have an established BTRIS user account for access to identified data. These accounts are given to all Principal Investigators or with permission to their designees. If you do not have an account, please complete the BTRIS Access form.

For additional information on these sessions, go to the BTRIS webpage.

Explore the New Web of Science interface with a refreshed look, enhanced workflow tools, faster page loads and more. Web of Science is a database providing access to billions of cited references, dating back to 1900 in the areas of life sciences, social sciences, arts, and humanities. This session provides a tutorial in using Web of Science, developing and executing searches on topics and citations, and managing results. 

Conducting a systematic review can be time consuming and challenging. This class provides an overview of the different steps in the comprehensive process of conducting a systematic review. At the completion of the class, participants will be able to identify each step of the systematic review process and know where to access valuable resources.

Conducting a systematic review can be time consuming and challenging. This class provides an overview of the different steps in the comprehensive process of conducting a systematic review. At the completion of the class, participants will be able to identify each step of the systematic review process and know where to access valuable resources.

Umbrella reviews, sometimes referred to as review of reviews, are a review of other published systematic reviews and meta-analyses and are appearing more frequently in scientific literature. Umbrella reviews appropriately address a broad question on a topic when there are plenty of published reviews already available. The benefits of conducting an umbrella review are to help synthesize the evidence for decision making in healthcare and explore inconsistencies and biases. This introductory class will share best practices and review the methodological steps required to conduct a rigorous, effective umbrella review.

UpToDate is an evidence-based clinical resource which includes collections of medical and patient education information, access to Lexi-Comp drug monographs, and a variety of medical calculators. It is the only clinical decision support resource associated with improved outcomes. Its primary purpose is to help physicians quickly locate information to answer their questions. This introductory session will demonstrate the major features of the database and will provide a hands-on tutorial on how to search by disease, symptom, lab abnormality, drug, or procedure. The class will also demonstrate how to access search history, create and view bookmarks, and claim credits for Continuing Professional Development (CME). Audience: Physicians, nurses, nurse practitioners, researchers, clinical fellows, post-docs, and trainees.

Web of Science is a database providing access to billions of cited references, dating back to 1900 in the areas of life sciences, social sciences, arts, and humanities. Reference materials include journals, books, reports, and conference papers. This introductory hands-on class provides a tutorial in using Web of Science, developing and executing searches on topics and citations, and managing results. Participants will also learn how to access citation information.

Researchers today face an almost overwhelming flood of scientific literature in various formats. How does one keep up? There are resources that can help filter and organize the information. This workshop will provide a close look at (1) a database of recommended biomedical research article (Faculty of 1000 (F1000); (2) citation tracking (Scopus and PLOS); (3) customized database alerts (NLM My NCBI); journal reading and table of content apps (BrowZine); and (4) social media tools (Twitter). Information focused on your interests will be readily available. Make keeping up a seamless part of your research workflow. Learning Objectives: identify resources to help find and filter scientific literature; learn how to use F1000, Scopus, PLOS, BrowZine, and Twitter for keeping up in your field of interest; and learn to use these resources as part of research flow.