Course Catalog

In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a review of core concepts in epidemiology. This session will cover the principles of epidemiology, key concepts and terms, brief review of outbreak investigations and study designs, and commonly used statistics in epidemiology (e.g., morbidity and mortality rates; incidence and prevalence; relative risk; odds ratio; sensitivity and specificity). The instructor will present a set of exercises to work through during the lesson (a calculator will be needed). 

The National Health and Nutrition Examination Survey (NHANES) is a program of studies designed to assess the health and nutritional status of adults and children in the United States. NHANES is a major program of the National Center for Health Statistics (NCHS), part of the Centers for Disease Control and Prevention (CDC). This introductory one-hour webinar by Jane Gwira Baumblatt, MD, MPH,  will provide an overview of the content of NHANES and how to access the data. 

This class will provide a demonstration of different options for cell type classification and treatment group comparisons at different levels with multiple samples of Single Cell RNA-Seq data. A CITE-Seq data will also be used to illustrate how to integrate protein and RNA information. Attendees will also learn how to integrate histology information with gene expression profile using a Spatial transcriptome data set. Partek Flow is a web-based application for the analysis of next generation sequencing (NGS) including RNA, small RNA, and DNA sequencing. With an easy-to-use graphical interface and the ability to build custom analysis pipelines, Partek Flow enables users to carry out routine NGS data analysis using dozens of popular algorithms without writing codes or running command lines tools.  Attendees will need to have taken the Partek Flow Basic Components class before registering or be comfortable with Partek Flow.

By the end of this class, attendees will be able describe how to access Partek Flow from the NIH Library, demonstrate how to combine cell type classification among different samples, perform cell type abundance analysis, identify batch removal options, conduct CITE-seq data and spatial transcriptomics data analysis, and create publication-ready visualization

Embase is a biomedical and pharmacological database covering international literature from 1947 to present. Embase includes citations and unique indexing for drugs not found in PubMed. This advanced training session will focus on using Embase for general literature searching, and will cover how to use the database’s embedded tools to design advanced queries for systematic reviews and adverse drug reactions. Participants will also learn how to combine queries to increase search precision, and how to use the PICO (population, intervention, comparison, and outcome) and the PV (Pharmacovigilance) wizards.

This first of five webinars will introduce NIH’s All of Us Research Program, including the program’s mission and core values. Learn about the current size and diversity of the participant cohort and the data types and tools available to researchers. Attendees will also see examples of recent research using the All of Us dataset. 

Presenter: Sheri Schully, Ph.D., is the deputy chief medical and scientific officer and the lead for ancillary studies in the All of Us Research Program at the National Institutes of Health. Through her leadership, she is establishing ancillary studies as a core and scalable capability of the program that will expand the cohort and deliver new phenotypic, lifestyle, environmental, and biological data to the All of Us Researcher Workbench. Dr. Schully has been involved with shaping the program and setting the scientific vision and strategy since its inception. Dr. Schully's research interests include genomics, personalized medicine, and the integration of genetic and genomic information into clinical and public health practices. Her work has been published in numerous high-impact scientific journals.

This is the first of five sessions about NIH’s All of Us Research Program and Researcher Workbench. Attendees are encouraged, but not required, to attend all sessions. Register for additional sessions below: 

• Session 1 - March 29: Introduction to the All of Us Research Program and Research Hub
• Session 2 - April 12: All of Us Researcher Workbench Registration
• Session 3 - April 19: Diving into the Researcher Workbench Data
• Session 4 - April 26: Introduction to Coding in the Researcher Workbench
• Session 5 - May 3: Resources to Support Researchers

*** All of Us Researchers Convention: April 3-4, 2024***
Researchers are invited to attend the All of Us Researchers Convention, April 3-4. The free, virtual event provides an opportunity for researchers who use All of Us data to showcase their work for others who share their interests in precision medicine. Register for the All of Us Researchers Convention at ResearchAllofUs.org/2024Convention.

This session will outline the All of Us Researcher Workbench registration process for NIH researchers. Access to the Researcher Workbench is free, and all registered researchers are provided $300 initial computational credits. Some analyses in the cloud may incur additional costs beyond these credits. Attendees will also learn how to create a Google billing account in case they use up their initial credits. Finally, attendees will hear about funding opportunities that can support using the All of Us dataset. 

Presenter: Brandy Mapes, Assistant Director of Operations
Brandy Mapes is an Assistant Director at the Vanderbilt Institute for Clinical and Translational Research (VICTR), specializing in strategic planning and implementation of national research programs including past work on NHGRI’s eMERGE Network and NCAT’s Clinical and Translational Science Awards (CTSA) program. Her current portfolio includes the All of Us Research Program’s Data and Research Center (DRC) where she has led efforts to develop and implement researcher education, training, and outreach programs as well as methods for participant survey and accompanying research support material development. In addition to All of Us, she also supports Vanderbilt’s local biorepository program, BioVU.

This is the second of five sessions about NIH’s All of Us Research Program and Researcher Workbench. Attendees are encouraged, but not required, to attend all sessions. Register for additional sessions below: 

• Session 1 - March 29: Introduction to the All of Us Research Program and Research Hub
• Session 2 - April 12: All of Us Researcher Workbench Registration
• Session 3 - April 19: Diving into the Researcher Workbench Data
• Session 4 - April 26: Introduction to Coding in the Researcher Workbench
• Session 5 - May 3: Resources to Support Researchers

In this webinar, attendees will learn the basics of using the All of Us Researcher Workbench’s point-and-click research tools, including how to create a workspace, how to build a cohort of All of Us participants using the Cohort Builder, and more. 

Presenter: Dr. Michael Lyons, Scientific Research Project Manager
Michael Lyons is a scientific project manager for Vanderbilt University Medical Center and is a member of the Outreach team at the All of Us Research Program’s Data and Research Center (DRC). He received his PhD in microbiology and immunology from Stanford University and is interested in applying his scientific background and knowledge in a translational setting that will benefit patients. As a part of All of Us, Dr. Lyons focuses on helping researchers utilize the program’s diverse resources for their own research needs. Additionally, he develops beginner training materials aimed at broadening the audience of researchers able to engage with the All of Us dataset and expanding the impact the program can have on personalized healthcare.

This is the third of five sessions about NIH’s All of Us Research Program and Researcher Workbench. Attendees are encouraged, but not required, to attend all sessions. Register for additional sessions below: 

• Session 1 - March 29: Introduction to the All of Us Research Program and Research Hub
• Session 2 - April 12: All of Us Researcher Workbench Registration
• Session 3 - April 19: Diving into the Researcher Workbench Data
• Session 4 - April 26: Introduction to Coding in the Researcher Workbench
• Session 5 - May 3: Resources to Support Researchers

Webinar attendees will hear tips and tricks to code efficiently in the Researcher Workbench using R and RStudio. Although Python and SAS are alternative programming languages available on the Researcher Workbench, this session will only focus on using R and RStudio. Participants should already have a general understanding of how to code in R prior to attending the session. This session will not cover the basics of coding in R.

Presenter: Aymone Kouame is a Data Scientist at Vanderbilt University Medical Center. She leads the Data Science & Engineering efforts for Digital Health Technologies (Fitbit). She is involved in the back-end and front-end processes of the All of Us Researcher Workbench curated data repository, working closely with the Curation and the Research Support Teams. Aymone discovered her passion for Data Science after a few years working/studying in Business and Accounting. She holds Master Degrees of Science in Data Analytics, Information Systems, and Accounting and Business Management. Before VUMC, she worked on the Data Science team of a cyber security company.

This is the fourth of five sessions about NIH’s All of Us Research Program and Researcher Workbench. Attendees are encouraged to attend all sessions. Register for additional sessions below: 

• Session 1 - March 29: Introduction to the All of Us Research Program and Research Hub
• Session 2 - April 12: All of Us Researcher Workbench Registration
• Session 3 - April 19: Diving into the Researcher Workbench Data
• Session 4 - April 26: Introduction to Coding in the Researcher Workbench
• Session 5 - May 3: Resources to Support Researchers

Webinar attendees will learn how to use and navigate the All of Us Researcher Workbench’s User Support Hub, which provides video tutorials, help articles, and more. Attendees will also learn about opportunities to get support from the Researcher Workbench help desk and how to stay involved with the All of Us Research Program through the program’s network of partners. 

Presenters:

Rubin Baskir, Ph.D., Researcher Engagement and Outreach Branch Chief, All of Us Research Program
Rubin Baskir, Ph.D., is a Program Officer and the Researcher Engagement and Outreach Branch Chief within the NIH All of Us Research Program engagement team. He is excited to be working with a team that helps maintain the essential relationship between the program, participants, and community partners.  Prior to his current position, Baskir began working in the All of Us Research Program as part of an American Association for the Advancement of Science (AAAS) science and technology policy fellowship. His interest in health policy began during his graduate work at Vanderbilt University, where, in addition to researching mechanisms of disease and signal transduction, he gained an appreciation for the effects of policy on human health. Baskir received his doctorate in clinical and cellular biology from Vanderbilt University and his Bachelor’s degree in biology from Washington University in St. Louis.

Sydney McMaster, CHES, Program Officer, All of Us Research Program
As a passionate health equity advocate, Sydney McMaster has served as a Program Officer and Researcher Engagement Specialist for the NIH All of Us Research Program for over two years. In this role, she functions as a liaison between the researcher community and the national program, offering support and technical assistance to researchers interested in studying the program’s dataset. Prior to this role, Sydney served as a Public Health Analyst with the Health Resources and Services Administration (HRSA) for three years. As a previous participant in a pathways internship program with HRSA, Sydney is passionate about supporting equitable pathways for diverse professionals interested in research and public health careers. 

This is the fifth of five sessions about NIH’s All of Us Research Program and Researcher Workbench. Attendees are encouraged, but not required, to attend all sessions. Register for additional sessions below: 

• Session 1 - March 29: Introduction to the All of Us Research Program and Research Hub
• Session 2 - April 12: All of Us Researcher Workbench Registration
• Session 3 - April 19: Diving into the Researcher Workbench Data
• Session 4 - April 26: Introduction to Coding in the Researcher Workbench
• Session 5 - May 3: Resources to Support Researchers

This one-hour online training will cover NatMed Pro, a database available through the NIH Library. NatMed Pro provides evidence-based information on natural medicines designed to improve clinical understanding of integrative medicine, natural therapies, and dietary and herbal supplements.

By the end of this training, attendees will be able to:

• Describe how to access NatMed Pro database via the NIH Library
• Use search functions and tools to locate information in the NatMed Pro database
• Share information via email from the NatMed Pro database with colleagues at NIH

Attendees are not expected to have any prior knowledge of the NatMed Pro database to be successful in this training.

This one and a half hour online training will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell RNA-Seq analysis pipeline. Partek Flow is a web-based application for the analysis of next generation sequencing (NGS) including RNA, small RNA, and DNA sequencing. With an easy-to-use graphical interface and the ability to build custom analysis pipelines, Partek Flow enables users to carry out routine NGS data analysis using dozens of popular algorithms without writing codes or running command lines tools.  Attendees will need to have taken the Partek Flow Basic Components class before registering or be comfortable with Partek Flow.

By the end of this training, attendees  will be able to:

• Describe how to access Partek Flow from the NIH Library
• Discuss the Quality Control (QC) and Quality Assurance (QA) tools
• Normalize data
• Descriptions options for cell type classification
• Perform differential analysis

Requirements

Access to the NIH Library Partek Flow requires two accounts:

1. Attendees will need to have taken the Partek Flow Basic Components class before registering or be comfortable with Partek Flow.
2. Access any of the NIH HPC resources require an NIH HPC account. NIH HPC accounts are restricted to NIH employees and contractors as determined by inclusion in the NIH Enterprise Directory. You can request an account from NIH HPC Account page. 
3. You also need to register for a Partek Flow account through the NIH Library.

Note on Technology

Registrants will receive an email with information and instructions to verify Partek Flow before the class. If you register the day before the class, you may not have time to secure access to Partek Flow. If you do not have the software installed, this training will be demo only.

This class focuses on structuring spreadsheet data so that it is ready for data analysis, or for importing into R or Python. By the end of this class, students should be able to: describe best practices for data entry, and formatting data in spreadsheets; list common formatting mistakes; describe different approaches for handling dates in spreadsheets; identify tips for quality control and data manipulation in spreadsheets; exporting data from spreadsheets.

Biosketches are used more and more in NIH internal reports. Participants will learn how to create a Biosketch with efficiency. Participants will also learn the appropriate components needed to put their best foot forward.

Learn how to use the Biomedical Translational Research Information System (BTRIS) to streamline the task of gathering and reporting active protocol data. BTRIS staff will demonstrate how to run queries in BTRIS and then guide attendees through running reports for their protocols.

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.

This one and a half hour online training  will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek Flow is a web-based application for the analysis of next generation sequencing (NGS) including RNA, small RNA, and DNA sequencing.  With an easy-to-use graphical interface and the ability to build custom analysis pipelines, Partek Flow enables users to carry out routine NGS data analysis using dozens of popular algorithms without writing codes or running command lines tools.

By the end of this training , attendees will be able to:

• Describe how to access Partek Flow from the NIH Library
• Discuss the Quality Control (QC) and Quality Assurance (QA) tools
• Identify pre- and post-alignment tools
• Describe options for quantification and normalization
• Perform pathway analysis and visualization

Requirements

1. Attendees will need to have taken the Partek Flow Basic Components training before registering or be comfortable with Partek Flow.
2. Access any of the NIH HPC resources require an NIH HPC account. NIH HPC accounts are restricted to NIH employees and contractors as determined by inclusion in the NIH Enterprise Directory. You can request an account from NIH HPC Account page. 
3. You also need to register for a Partek Flow account through the NIH Library.

Note on Technology

Registrants will receive an email with information and instructions to verify Partek Flow before the class. If you register the day before the class, you may not have time to secure access to Partek Flow. If you do not have the software installed, this training will be demo only.

Choosing a quality journal to publish in can be a daunting task. In this class, participants will become familiar with the available resources and tools to assist in targeting quality journals, as well as ways to recognize questionable or predatory journals. Additional topics include tips to avoid a predatory conference, evaluating invitations to serve as a peer review or editorial board member, preprint servers, and what to do if you published with a questionable journal will be covered.

This class will give you an in-depth look at tools for evidence-based clinical information.  Explore our available resources and learn search tips for DynaMed (clinical decision support tool), Access Medicine (decision making tool), Cochrane (evidence to inform healthcare decisions), EBMcal (clinical criteria sets and decision tree analysis tools), and PubMed shortcuts to evidence based clinical information. Learning Objectives: become familiar with the NIH Library’s clinical resource tools and know how to use them; and do better, more efficient searching using clinical resource tools.