Instruction Menu

Below is a list of instructional offerings from the Medical Library. To request an instruction session for your group, please contact Caitlin Meyer (caitlin.meyer@yale.edu).

Module	Learning Objectives	Duration (min)	Category	Add-on Module
Introduction to Genome Browsers: Part 2 UCSC Genome Browser	View gene structure and retrieve sequences Add and remove tracks Explore phenotype and literature track Find and retrieve variation data Find and retrieve genes located in a genomic region	120	Bioinformatics
Making Sense of Genomic Variation: Part 1 SNP Annotation	Learn how to annotate variations using dbSNP, Online Mendelian Inheritance in Man, GWAS Catalog, EBI-Ensembl Variant Effect Predictor	120	Bioinformatics
Introduction to Functional Analysis of Omics Data: Overrepresentation Analysis (ORA) using public online tools	Understand the components of an ORA: gene list, cutoffs, background, or reference set, etc Explore statistical vs biological (or study) results Visualize and present results	120	Bioinformatics
Introduction to Functional Analysis of Omics Data: Gene Set Enrichment Analysis (GSEA)	Prepare your data and files for running GSEA Learn about Molecular Signature Database (MSigDB) Run GSEA analysis and the Leading edge analysis and results interpretation Send and visualize the results using the Enrichment Map app	120	Bioinformatics
Introduction to Annotation of Gene Expression Data	Learn basic concepts/vocabulary for transcriptomics analysis. Find the right assembly or reference genome to use in their analysis Different types of genomic annotations and what tools using to annotate datasets Use Enbsembl Biomart and NCBI datasets, and other tools to batch annotate lists	120	Bioinformatics
Find, Download and Transform Public Bulk RNA Seq Data to Analyze with DESeq2 in RStudio	Search and download bulk RNA-seq data available on GREIN - GEO RNA-seq Experiments Interactive Navigator Process GREIN data tables to be analyzed by DESeq2 in RStudio Load R packages (e.g. DESeq2) Setup data to run DESeq2	120	Bioinformatics
Upload Bulk RNAseq Data Tables into RStudio and Setup a DESeq2 Analysis	Use R packages readr to import data tables into RStudio Use basic R functions such as view() and str() to visualize and inspect data Import R package DESeq2 into RStudio Assemble a DESeq2 data frame and design a differential gene expression analysis Run the function DESeq() and brief introduction to the function results()	120	Bioinformatics
Manipulate DESeq2’s Results() and Plot Functions	Use DESeq2 function resultsNames() to retrieve the different comparisons that were setup in DESeq2 analysis design Use the argument contrast = within the function results() to retrieve the results of comparisons between specific groups in a study with 4 groups Use functions plotPCA(), MAplot() and plot() as basic tools to visualize data analyzed with DESeq2 package	120	Bioinformatics
Analysis of differential gene expression of bulk RNA-seq data using “DESeq2” in RStudio	Import data files into RStudio Load R packages Run “DESeq2” Save processed data files into your computer (e.g. normalized counts, DEX genes table) Perform basic data visualization (e.g. PCA plot, MA plot)	120	Bioinformatics
Finding differential expressed genes using “DESeq2” in RStudio	Import data files into RStudio Load R packages Run “DESeq2” Save processed data files into your computer (e.g. normalized counts, DEX genes table) Perform basic data visualization (e.g. PCA plot, MA plot)	120	Bioinformatics
Gene annotation using "biomaRt" in R/RStudio	Import data files into RStudio Load R packages Setup a "biomaRt” query Perform basic data manipulation (e.g. add and re-order columns in a data frame) Save processed data files into your computer	120	Bioinformatics
Intro to R for Bioinformatics	Basic data format and type in R Base R functions Basic data manipulation and inspection Install R package such as Readr Import .csv files using function read.csv()	120	Bioinformatics
Network Analysis of Omics Data with Cytoscape	Create networks from file, importing networks from public databases Merge networks, grouping nodes Visualize expression (e.g. transcriptomics, proteomics) data on networks Find and download applications Use MetScape for visualization and interpretation of metabolic and expression profiling data	120	Bioinformatics
Introduction to Genome Browsers. Part 1 Ensembl	Learn the basic functionalities and navigation of Ensembl by using specific examples Annotate omics data using BioMart interface Retrieve data and information from the browser	120	Bioinformatics
Personalize Zotero for Maximum Efficiency	Personalize their Zotero installation Describe and use many advanced Zotero features	60	Citation Management
Managing Citations and Manuscripts with EndNote	Build and organize an EndNote library with references from various resources Locate article PDFs efficiently with Find Full Text Integrate EndNote into Microsoft Word for easy manuscript formatting	45	Citation Management	Comparison to other citation management tools (15 min)
Thesis Support: Managing Your Research	Understand the importance of using citation management tools and strategies Compare EndNote and Zotero to best serve your thesis needs Identify and locate citation export options in major databases Use “cite while you write” features	60	Citation Management
Advanced EndNote	Options for sharing EndNote libraries with colleagues Customizing or modifying a journal output style to meet the citation requirements of a journal Creating "Smart Groups" and "Groups from Groups" to search your EndNote library effectively	45	Citation Management
EndNote Imports	Import batches of records from any bibliographic database	30	Citation Management
Zotero in 30 minutes	Build and organize a Zotero library with references from various resources Locate article PDFs efficiently Integrate Zotero into Microsoft Word and Google Docs for easy manuscript formatting	30	Citation Management
How I Organize My Intellectual Life with Citation Management Software	Organize citations in their library with collections, saved searches, groups, and tags Retrieve additional information about articles through plugins Rearrange the default library display Run simple and advanced searches of records, PDFs, and snapshots	60	Citation Management
Where Are You Going to Put That? How to Share Your Data	Find and select data repositories Prepare your data for deposit Share data for maximum reuse	60	Data & Programming
Cleaning and Transforming Data with Python: An Introduction to pandas (Python, Part 3)	Determine what you want to achieve with data cleaning Work with pandas data structures (dataframes, series) Perform routine data cleaning tasks with pandas (e.g., dealing with missing data, converting data types, cleaning up text issues, etc.) Determine whether and what data transformation (e.g., grouping, subsetting, reshaping) might be needed for further analysis	120	Data & Programming
The Very Basics of the Unix Command Line	Overview and fundamental concepts of the Unix command line Accessing and navigating a Unix system with a terminal Essential command line tools for reading, editing, and searching files Fundamentals of the Unix file system permissions Automating tasks with shell scripting Software management via the command line	90	Data & Programming
Fulfilling New Data Management & Sharing Expectations: The New NIH Policy and Beyond	Understand the main components of the NIH Data Management and Sharing Policy (launched January 2023), plus additional related policies Describe how to write and submit data management and sharing plans, with an emphasis on complying with NIH guidelines Compare and evaluate various strategies for managing and sharing data, including data standards and data repositories	60	Data & Programming
Getting Started with HTML and CSS	Basic understanding of HTML/CSS and how it's used to create websites The process for creating a rudimentary webpage How to style the webpage using CSS declarations	45	Data & Programming
Choosing the platform for your GIS project	ArcGIS Desktop/Online SimplyMap PolicyMap CartoDB Open source software for geospatial analysis	60	Data & Programming
Create online surveys using Qualtrics	Features of the software Designing your own questionnaires Using the online data tools	45	Data & Programming
Managing Research Data	Articulate why research data management is important, and how it can improve your project Understand best practices in research data management Learn how to write a data management plan (DMP)	90	Data & Programming
Getting Started with Python: An Introduction to Programming (Python Part 1)	Write your first program (“Hello, world!”, printing) Deal with mistakes (error handling) Work with text and numbers (strings, integers, floats, variables, assignment, concatenation) Store lots of numbers and/or text (lists, dictionaries) Integrate conditions and repetition into code (if-else statements, loops) Combine above elements together in a final mini project	120	Data & Programming
Analyzing and Visualizing Data with Python: An Introduction to numpy and matplotlib (Python Part 2)	Import and use Python libraries Read tabular data into Python Perform basic statistical operations on the data Create basic plots from the data Process and plot multiple data files at once	120	Data & Programming
Where in the World is the Data You Need? How to Find and Reuse Data	Articulate data needs based on a research question Locate and appraise datasets Examine real-world data	60	Data & Programming
Design Basics: How to Create Better Visuals	Understand the importance of colors, fonts, and layout Recognize and identify common pitfalls in 'bad' graphic designs Come away with a list of free graphic design tools available on the web	45	Design	Photoshop Basics: How to Create a Digital Sign (30 min)
Photoshop Basics: How to Create a Digital Sign	Explore basic Photoshop tools and capabilities How to insert an image, overlay text, and adjust for readability Export a file suitable for a digital sign	45	Design
Visualizing Information: Designing Effective Posters and Figures	Learn the basic principles of assembling an academic poster including recommendations for font, layout, and color usage Learn the basic principles of creating academic figures and visualizations to represent data, including analysis of various examples Understand pre-work required before creating figures and visualizations Discover free tools, resources, and support for creating the best representation of your research	45	Design	Data Processing and Cleaning: A Brief Overview & Tutorial (20 min); Preserving Your Information: A Brief Tutorial on Repository Deposits (10 min)
Using Special Collections at Yale University	Medical Historical Library Maps Collection Divinity Special Collections Beinecke Rare Book and Manuscript Library	30, 45, 60	General
Literature Reviews in 60 Minutes	Choose a type of review Pick appropriate bibliographic databases Brainstorm search terms Manage citations Plan notetaking and critical appraisal processes	60	Literature Searching
Foundations of Evidence-based Practice Tools	Write a well-built clinical question and transform it into a search strategy Utilize different strategies and tools for highly precise literature searching Compare and contrast searching the primary literature vs evidence-based practice mobile applications Critically engage with search results	45, 60, 75	Literature Searching
Nutrition and food systems literature in specialized bibliographic databases: AGRIS and AGRICOLA	Predict whether AGRIS or AGRICOLA is likely to include literature relevant to their information needs Use controlled vocabulary terms from the NAL and AGROVOC thesauruses to retrieve relevant results Refine and filter search results to find a small set of highly-relevant documents Navigate to the full text of documents retrieved in AGRIS or AGRICOLA searches	60	Literature Searching
Asking Clinical Questions & Acquiring the Best Evidence	Formulate a well-built clinical question with PICO Construct a concept table and literature searching strategy Review levels of evidence and unfiltered vs filtered information Perform a search in PubMed	45, 75	Literature Searching	Additional databases (10 min each)
Advanced Literature Searching in PubMed	Describe the differences between MEDLINE and PubMed Central. Compare and use MeSH hierarchy and subheadings Identify and use field searching and automatic term mapping Create NCBI alerts Perform advanced searches in PubMed	45	Literature Searching
Beyond PubMed: Expanding your research toolkit	Describe the scope of content in PubMed Compare general and specialty academic databases Leverage unique functions (searching, filtering, sorting) across platforms Perform advanced searches in multiple databases	45	Literature Searching
Searching with the PubMed	Identify PubMed’s features and search tools Locating options to manage your results and export citations Execute steps to save your search results and set up alerts Execute a successful retrieve of full text	45	Literature Searching	Searching the Literature with PubMed (45 min)
Foundations of Critical Appraisal of Evidence	Define the goals of critical appraisal Explore common tools for assessing evidence Practice appraising a randomized controlled trial	45	Literature Searching
Beyond PubMed: Searching the APA PsycInfo Database in 30 minutes	Formulating your question using PICO for an effective search in APA PsycInfo Build a search using keywords Incorporate the use of Boolean operators to connect your concepts Learn to use search syntax	30	Literature Searching
Hacking Your Research with Medical Subject Headings (MeSH terms)	Identify potential collaborators or mentors at Yale Quickly locate relevant literature Use known articles to find additional literature to inform your work	45	Literature Searching
Searching MEDLINE on the Ovid Platform	Formulating your question using PICO for an effective search in Ovid Build a search using MeSH terms and keywords Incorporate the use of Boolean operators to connect your concepts Learn to use specialized search syntax (truncation, wildcards, adj)	45	Literature Searching	Managing your results using EndNote (30 min)
Thesis Support: Selecting Databases	Describe the purpose of searching a variety of databases Outline major biomedical databases Compare content in major databases Correctly search using keywords and controlled vocabulary for your concept table Translate searches from one database to the next	60	Literature Searching
Asking a Good Questions and Preparing to Search	Constructing and parsing a research question Boolean logic Proximity operators Field searching Controlled vocabularies and database structure	60	Literature Searching
Searching with Google and Google Scholar for the Health Sciences	How to Search Google effectively and precisely How to use advanced search features and tools How to evaluate your results	45	Literature Searching	Managing your results using EndNote (30 min)
Thesis Support: Your Research Question	Describe the importance of a strong research question Identify methods for exploring existing literature Understand the difference between keywords and controlled vocabulary Produce a basic concept chart from your research question	60	Literature Searching
Beyond UpToDate: Tour of the Biomedical Literature Databases	Scopus Web of Science Databases on the Ovid platform (including PsycInfo and Embase)	60	Literature Searching
Beyond PubMed: Web of Science	Formulating your question using PICO for an effective search in Web of Science Build a search using keywords Incorporate the use of Boolean operators to connect your concepts Learn to use specialized search syntax specific to this database (truncation, wildcards, NEAR, etc.)	45	Literature Searching	Managing your results using EndNote (30 min)
Literature Searching for Health Professions Education (HPE) Scholarship	Discuss how HPE scholarship differs from other forms Frame and create an answerable HPE research question Identify essential resources to query for HPE searches Search using controlled vocabulary and/or keywords Evaluate results	45, 60	Literature Searching	Managing your results using EndNote (30 min)
Identifying Quality Sources of Information	Learn to recognize factors that may indicate a journal is predatory. Identify trustworthy indexing sources. Learn to use tools to match a research topic to a journal. Understand the difference between PubMed and PMC.	45, 60, 75	Literature Searching
Demonstrating approaches to finding additional relevant documents	Decide whether and how to do citation chaining Find other papers using the same instrument Find other papers with similar keywords/indexing Find related interim research products (preprints, grants, conference papers, code, datasets....)	30, 45, 60	Literature Searching	Manage and share a library of citations (20 min)
Evidence-Based Clinical Information Skills (YSM Elective)	Identify key resources for access to reliable, evidence-based medical and health sciences information Articulate focused and answerable research and clinical questions Develop skills to access, retrieve, appraise, and manage information for clinical purposes and patient care Evaluate and critically appraise information related to a topic to be determined with student(s) Synthesize and present their findings and experiences throughout the elective to their cohort	120	Literature Searching
Medical Research in the News	Identify news coverage of and social media reaction to biomedical research Compare popular and scholarly discourse Cite grey literature Evaluate grey literature	15, 30	Literature Searching
Expand your Literature Searching with Embase	How to conduct effective literature searches in Embase How Embase compares with MEDLINE	60	Literature Searching
Before You Write the Review: How to Effectively Read and Annotate Scholarly Literature	Define ‘annotation,’ and explain how it applies to the research/review process Take notes about key areas of a source document-- some universal and some specific to their research topic (descriptive vs. analytical annotation) Explain the difference between scholarly and grey literature.	60	Literature Searching
Find, Save, and Read Global Health Literature Like a Pro	Explain the difference between scholarly and grey literature, and devise search strategies to find both kinds of information (pertaining to a global health research interest). Download and add a citation to Zotero or EndNote. Take notes about key areas of a source document.	60	Literature Searching
GIS Series: Searching Geospatial Literature	Find published and grey literature about applications of GIS in biomedical research Strategies for searching for geospatial topics in biomedical databases (PubMed, MEDLINE, Embase), broad databases (Web of Science, Scopus), engineering databases (SPIE Digital Library and RESORS), and Esri’s GIS bibliography	60	Literature Searching	Working with census data for social determinants of health (60 min), Choosing the platform for your project (60 min)
Grey (Lit) Matters	Define grey literature Evaluate search strategies for grey lit Identify grey lit databases and their appropriate use Assess and demonstrate use of Advanced Google and Custom Searches	30	Literature Searching
Health Information for Your Patients	Identify freely available consumer health resources Evaluate consumer health information Describe the information needs of their patients	45	Literature Searching
Interdisciplinary Lit Searching: PubMed and Lens	Create and refine searches in PubMed and Lens, using Boolean operators and searching specific fields Explain why some articles are discoverable in Lens, but not PubMed Ascertain from the NLM Catalog whether a given journal’s content is fully discoverable in PubMed Generate visualizations of PubMed and Lens data using online tools Export records from PubMed and Lens to citation managers	60	Literature Searching
Leverage Literature Reviews as a Public Health Practitioner	Find and evaluate “filtered” and “synthesized” evidence Distinguish between the intended use of different types of evidence synthesis papers (like systematic reviews, scoping reviews, reviews of reviews, and rapid reviews) Access the full text of review papers, even if you don’t have academic medical library subscriptions in the future	60	Literature Searching
Library Orientation	Identify library services and resources Summarize ways to access the library Recall steps to connect to resources off-campus Describe the role of the library as it relates to your work/education	15, 30, 45, 60, 75	Orientation
Navigating the NIH Manuscript Submission Process	How to submit, review, and approve your manuscript in the NIHMS	60	Scholarly Communication
Open Access	What is open access Publishing your research open access	60	Scholarly Communication
Preparing to Publish	How to create a persistent author identifier using tools such as ORCID Understand different citation management tools Identify pertinent metrics to help decide on journals to submit your paper Understand different ways to disseminate your manuscript beyond journals	60	Scholarly Communication
Grant Reporting, Compliance and Application (biosketch) through MyNCBI	Ccreate MyNCBI account and how to link it to the eRA Commons account Delegate your account Populate and manage My Bibliography Use My Bibliography for grant reporting/compliance Use SciENcv to create different biosketches (from scratch, from external source, etc) Create an ORCID ID and link it to SciENcv	60	Scholarly Communication
Research Impact Basics	Distinguish between author impact, article impact, and journal impact Identify common metrics used to gauge impact Use key tools to track, measure, and visualize research impact Deploy strategies to increase your personal impact	30	Scholarly Communication
My Bibliography and SciENcv: Grant reporting, compliance and biosketch through MyNCBI	How to create MyNCBI account and how to link it to the eRA Commons account How to delegate your account How to populate and manage My Bibliography How to use My Bibliography for grant reporting/compliance	45	Scholarly Communication
Update Your Research Profiles	Add works to a research profile such as ORCID Learn which research profile meets their needs	60	Scholarly Communication
Enhancing Research Impact	Introduction to the landscape of research impact and how it relates to your research, relationships, and outcomes	60	Scholarly Communication
What Does it Mean to Publish My Work ‘Open Access’?	Explain what open access means, and what OA incentives exist at Yale to a friend. Use web tools/platforms such as DOAJ, OSF, and EliScholar to find information about an OA journal or upload their work to preprint server/repository, respectively. Recall policy changes of the NIH and OSTP that encourage openness of taxpayer-funded research— past, present & forthcoming (i.e. NIH Public Access Mandate, 2008 & OSTP Memo, effective 2025).	60	Scholarly Communication
Finding and tracking your research impact	Identify databases that track research impact Understand h-index and other bibliometric tools Create account and save searches in Scopus and Web of Science	30	Scholarly Communication
Keeping Current with the Literature: Saving Searches & Creating Alerts in PubMed	Create an NCBI account Save PubMed searches and results Set up an e-mail alert to automatically receive new articles on a given topic	30	Scholarly Communication	Scopus (30 min), Web of Science (30 min)