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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).
Modulesort descending Learning Objectives Duration (min) Category Add-on Module
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
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
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
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)
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
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
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)
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)
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)
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
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
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
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
Getting Started with Python: An Introduction to Programming (Python Part 1)
  • How to write your first program (“Hello, world!”, printing) 
  • How to deal with mistakes (error handling)
  • How to work with text and numbers in Python (strings, integers, floats, variables, assignment, concatenation)
  • How to store lots of numbers and/or text in Python (lists, dictionaries)
  • How to integrate conditions and repetition into code (if-else statements, loops)
  • How to put the above elements together in a final mini project
120 Data & Programming
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
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
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
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
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
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 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 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
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
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
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)
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
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)
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
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
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
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
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
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
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)
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)
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
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
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