The Human Gene Mutation Database (HGMD) database provides quick access to known published gene lesions responsible for human inherited disease. This session will explore how to query genes and mutations in HGMD and how to view the curated content.
QIAGEN’s Ingenuity Variant Analysis (IVA) has been replaced by QIAGEN Clinical Insight Interpret – Translational (QCII-T), which combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based on published biological evidence and your knowledge of disease biology. QCII-T allows you to interrogate variants from multiple biological perspectives, explore different biological hypotheses, and identify the most promising variants for follow-up. This class will focus on how to use QCII-T to upload datasets, efficiently use different filtering mechanisms to identify causal variants, and export data. Participants will also review feature changes migrating from Ingenuity Variant Analysis to QCII-T.
This course will present a brief overview of the scope and features of clinical/biomedical research information resources, including: PubMed; Embase; evidence-based and clinical trials databases; other information resources of value in high-impact clinical care; and opportunities to obtain additional detailed information and specific training.
Find answers to many questions about information resources, including: Why is it important to search beyond PubMed for clinical information? Why would a researcher search Embase, Pharmaprojects, Cochrane, ToxNet and PsycINFO? When would a researcher use the “-“ operator in Google and Google Scholar?
Participants will receive an overview of information resources, search techniques, and strategies to find information in support of commercializing biomedical licensing opportunities. This class is offered as an integrated part of the FAES TECH565, Biomedical Business Development for Scientists. For a complete description see the FAES course catalog at www.faes.org.
Learn how to get started on using QIAGEN’s Ingenuity Pathway Analysis (IPA) to quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in tens of thousands of peer-reviewed articles. The class will demonstrate how to explore IPA's knowledge & discovery tools to relate the most recent literature findings to your research. The demo session will mainly focus on biological interpretation of expression data but will also cover multi-omics analysis including variant data and phosphoproteomics.
Getting Started: fundamentals of IPA; overview of key features; search & pathway building; advanced search; building & editing pathways; using Build & Overlay tools. Dataset Analysis: data upload & analysis; interpretation of gene, transcript, protein & metabolite data; pathway analysis & canonical pathways; downstream effects & interpreting the heat map; causal regulators and their directional effect on genes, functions and diseases across multiple time points or doses; interpreting networks; comparison & multiple observations analysis; miRNA and isoform analysis; BioProfiler: define relationships between molecule activity and diseases/processes in the literature. Q & A session: A QIAGEN Ingenuity Field Applications Scientist will be available to answer individual questions or discuss specific projects.
RNA-Seq and ChIP-Seq studies individually provide useful information on gene expression profiles and elucidating the genomic regions and target genes that bind one or more regulatory proteins, respectively. When viewed together, the integrated analysis of the two data types within a given experimental study can identify co-regulated genes that share a gene regulatory “framework”. This type of systems biology approach can yield useful information when elucidating the global mechanisms of disease pathology and developing therapies for treating human genetic disease.
This course is broken down into a morning session, followed by an opportunity for individual consults in the afternoon. NOTE: This is the second course in a two-part series and students must have attended the entire course to obtain maximum benefit from the training.
The morning session (typically 9:00 am-12:00 pm) will focus on the integration of the ChIP-Seq and RNA-Seq and will cover the topics of: identifying overlapping ChIP-Seq peaks with RNA-expression profiles; pathway analysis of correlated ChIP-Seq target genes; visualization of ChIP-Seq peaks with RNA-Seq expression profiles; transcription Factor Binding Site (TFBS) analysis of promoters from ChIP-Seq target genes; identifying conserved TFBS patterns in orthologous promoters; genome-wide analysis of promoters sharing a conserved regulatory network. The afternoon session (typically 1:30 pm-4:30 pm) will be dedicated to individual consults with NIH research investigators.
Adobe Premiere Pro, which is part of the Adobe Creative Cloud Suite, is video editing software for film, TV, and the web. This intermediate class will demonstrate advanced post-production techniques using this software. Participants will learn how to bring their video projects to the next level with graphics, popular effects, and audio editing. Previous experience with Adobe Premiere Pro is recommended.
This session will build a foundation for using Adobe Illustrator, a vector art tool available for use in the NIH Library Technology Hub. This introductory class is geared for participants new to Illustrator or for those interested in a refresher. The instructor will demonstrate software fundamentals, including working with colors and graphs, drawing and editing figures, and using layers.
This introductory class is geared for participants new to Adobe Photoshop or for those who need a refresher. This session will build a foundation for using Photoshop and understanding its most popular tools. Participants will become familiar with the Photoshop interface and commonly used features of this powerful design program. The instructor will demonstrate advanced fundamentals including working with layers and changing backgrounds.
Adobe Premier Pro, which is part of the Adobe Creative Cloud Suite, is the leading video editing software for film, TV, and the web. In this introductory class, participants will learn how to use this powerful tool to edit videos during post-production of video projects. The class will provide an overview of basic concepts for working with videos, during which participants will gain skills on how to import and edit video and audio files.
Artificial Intelligence (AI) and Machine Learning (ML) are hot topics today, but are already part of our everyday lives. This class will introduce the basic principles of AI and ML and the current state of this field. The instructor will share examples of AI used in common applications and health research. AI limitations and ethical considerations will also be discussed. This course is designed for individuals new to the topic or for those who need a refresher.
FireCloud (Powered by Terra) is a data analysis platform that contains a system of workspace functionalities centered on data sharing and analysis. Researchers can use FireCloud to perform a variety of analyses through two main mechanisms: batch workflow execution and interactive analysis (including data visualization). Workflow execution is achieved through a workflow management system called Cromwell, which is designed to be highly portable, capable of connecting to multiple computing platforms, and horizontally scalable. Interactive analysis is achieved through Jupyter notebooks or RStudio, which can be associated with a range of configurable runtime environments and incorporate various kernels and packages to support exploratory analyses of arbitrary scale and complexity.
In this hands-on session, we will introduce FireCloud to all attendees as a part of the NCI Cloud Resources. The participants will learn how to access key data sets such as TCGA and CPTAC and bring this data (or their own data) into a secure FireCloud workspace. Participants will also learn how to configure and launch workflows from their workspace and perform interactive analysis with applications such as Jupyter Notebooks, RStudio, and more. This session will also cover how billing operates in FireCloud and how to securely share the personal FireCloud workspace with collaborators.
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 presentation serves to introduce the concepts associated with the analysis of categorical data. The presentation will begin with a definition of categorical data and a review of some of its benefits and limitations. Then the presenter will introduce the idea of analysis via proportions in the framework of a contingency table. From here, the audience will then learn about some common types of inference that may be employed in this setting. The presentation will end with some examples of ways to effectively display categorical data and introduce some common statistical models that may be used with categorical data.Training Category: Data Services Classes
Introduction to Data Visualization in R: ggplot in R is the fourth class in the NIH Library Introduction to R Series. A basic understanding of R and R Data Types is expected. This class provides a basic overview of producing scatter plots, boxplots, and time series plots using ggplot. 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 Program 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: understand the basics of plotting in ggplot; demonstrate how to add a layer to a plot using ggplot; define ggplot aesthetics; add a geometric function to a plot; produce boxplots, and time series plots using ggplot; set universal plot settings; describe what faceting is and apply faceting in ggplot; modify the aesthetics of an existing ggplot plot (including axis labels and color); build complex and customized plots from data in a data frame; exporting a plot using ggplot.
Students are encouraged to install R and RStudio and download the class data before the class so that they can follow along with the instructor. Attendees will need to download the class data before the class.Training Category: Data Services Classes
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.
EndNote Online is a web-based version of EndNote, allowing the user to collect and organize references, and format citations and bibliographies automatically while you write your papers in Microsoft Word. In this introductory session, participants will learn how to create an EndNote online account, import references, create, manage, and share groups of citations, and insert formatted citations and bibliographies into a Word document using the "Cite While You Write" feature.
Mendeley is a reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research. This session will provide you with tips on how to get started with the NIH institutional version of Mendeley, migrate your libraries from other reference managers, collaborate with other researchers online using the social/researcher groups in Mendeley within/outside NIH. Mendeley allows you to: generate bibliographies, collaborate with researchers online, import papers from research software, and read papers on the go with our iOS and Android apps.
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.