The Cushing/Whitney Medical Library has prepared the following menu of training sessions for the winter semester. It includes training on how to do literature search, patent search, use of Cytoscape, genome browsers, EndNote, systematic reviews, functional analysis, variant annotation, and more. Since seating is limited, please register to reserve yours by following the links next to each session.
Please contact Vermetha Polite vermetha.polite@yale.edu for questions or comments on these sessions.
PubMed: Improve your Skills
Description: PubMed is one of the most comprehensive resources for searching the biomedical literature. Most researchers have used it at one time or another, but it may be time to brush up on your search skills to ensure that you a relevant set of results. In this class, we will go over PubMed search techniques, including how to quickly limit a search and the role of Medical Subject Headings (MeSH) in creating more effective searches. Participants will also learn timesaving features such as saving searches and how to link out to full-text.
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Date & Time: 5:00pm - 5:50pm, Thursday, February 4, 2016
Date & Time: 5:00pm - 5:50pm, Thursday, February 18, 2016
Date & Time: 12:00pm - 12:50pm, Friday, February 26, 2016
Date & Time: 5:00pm - 6:00pm, Wednesday, March 2, 2016
Date & Time: 5:00pm - 5:50pm, Tuesday, March 22, 2016
Date & Time: 5:00pm - 5:50pm, Wednesday, April 13, 2016
RefWorks Basics
Description: Learn basic features and use of this web-based citation management system, such as setting up a Yale account (no purchase required), exporting citations from external databases and importing them into your account, and using RefWorks with MS Word to create citations in context and bibliographies for your manuscripts. This class is one hour.
Date & Time: 12:00pm - 1:00pm, Wednesday, January 27, 2016
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Managing your References with EndNote
Description: EndNote is a citation-management software application that makes saving citations and then citing them within documents easy. EndNote's pre-formatted style templates, specific to journal instructions, make it easy to insert references into your papers as you write them. In this class you will learn how to easily add citations into your EndNote library, attach PDFs, and insert references into your research papers.
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Date & Time: 3:00pm - 4:00pm, Thursday, January 21, 2016
Date & Time: 5:00pm - 6:00pm, Wednesday, January 27, 2016
Date & Time: 2:00pm - 3:00pm, Friday, February 5, 2016
Date & Time: 5:00pm - 6:00pm, Wednesday, February 10, 2016
Date & Time: 5:00pm - 6:00pm, Wednesday, February 24, 2016
Date & Time: 5:00pm - 6:00pm, Tuesday, March 8, 2016
Date & Time: 2:00pm - 3:00pm, Wednesday, March 16, 2016
Date & Time: 1:00pm - 2:00pm, Friday, March 25, 2016
Date & Time: 5:00pm - 6:00pm, Thursday, April 7, 2016
Date & Time: 5:00pm - 6:00pm, Wednesday, April 27, 2016
Enhance your Library Skills
Description: Are you new to the Medical Campus? Need a refresher on how to use the Medical Library? Information experts will assist you in finding everything from books in the online catalog to locating peer-reviewed full-text articles including when and how to request materials through our Interlibrary Loan service. You will be surprised about the resources and services available to you.
Use the library catalog to find materials including books, prints, maps, and more
Decipher confusing citations
Find full-text articles
Identify article databases in your subject area
Distinguish when and how to request material through Interlibrary Loan
Identify your librarian
Date & Time: 2:00pm - 2:50pm, Thursday, January 28, 2016
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Tools for gene enrichment analysis
Description: Bioinformatics enrichment tools play an important role in identifying, annotating, and functionally analyzing large list of genes generated by high-throughput technologies (e.g. microarrary, RNA-seq, ChIP-chip). This workshop will provide an overview of the principle, type of enrichments, and the infrastructure of enrichment tools. By using concrete examples, it will also introduce some of the most popular tools for gene enrichment analysis such as DAVID, GSEA, and WebGestalt, as well as the proprietary softeare MetaCore.
Date & Time: 12:00pm - 1:30pm, Thursday, February 4, 2016
Location: SHM L Simbonis Room 101A Yale Medical Library, 333 Cedar St. New Haven CT 06520
Systematic Reviews: Conducting comprehensive searches
Description: One critical step in the SR process is to comprehensively search the literature. This workshop will introduce procedures to ensure that your search is comprehensive, methodical, transparent and reproducible.
Date & Time: 1:30pm - 3:00pm, Wednesday, February 10, 2016
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
The VERY Basics of the Unix Command Line
Description: A lot of biomedical software programs do not come with a graphical user interface (GUI), and a Unix command-line terminal environment is required to run such programs. In this 2-hour session, you will learn the basics of a Unix command-line terminal, such as how to navigate the file system, the permission and security structure, and how to run programs from the command line. No previous Unix or command-line experience is required to attend this session.
Free and open to any Yale University student, faculty and staff.
Registration required since the number of seats is limited.
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Date & Time: 2:00pm - 4:00pm, Thursday, February 11, 2016
Date & Time: 10:00am - 12:00pm, Thursday, April 14, 2016
Introduction to patents and patent searching
Description: Patents are challenging but important sources for product development and discovery of technical information. This workshop will provide a basic introduction to the patent literature and the United States patent process. We will look at tools and strategies for locating patents and intellectual property.
Date & Time: 2:00pm - 3:00pm, Friday, February 19, 2016
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Introduction to Genome Browsers
Description: In this workshop we will learn how to navigate the genome browsers from NCBI's Genome Workbench, UCSC Genome Browser, and Ensembl. These browsers are valuable tools when identifying, localizing genes, and looking at their information in the genomic context. By using concrete examples, it will be shown how to locate a human gene, download a gene sequence and its upstream sequence, locate Single Nucleotide Polymorphisms (SNPs) and conserved regions, and use the browsers to download results in a batch
Date & Time: 12:00pm - 1:30pm, Thursday, February 25, 2016
Location: Medical Library, Simbonis Large Conference Room 101A, 333 Cedar St, New Haven CT 06520
Cytoscape: Going from Raw Data to a Publishable Image
Description: These hands-on workshops will demonstrate the use of Cytoscape, an open source molecular interactions visualization tool. Cytoscape allows for the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data. One session, “Cytoscape: Going from Raw Data to a Publishable Image,” will cover core functions, such as learning how to import network and attribute data, change visual properties to easily distinguish biologically significant relationships, create a legend for the image, manually add nodes/edges, etc.
Date & Time: 9:00am - 12:00pm, Thursday, March 3, 2016
Location: C-103 - SHM 333 Cedar St, New Haven CT 06520
Presenter: Marci Brandeburg, University of Michigan.
Cytoscape apps with a Focus on MetScape
Description: This hands-on workshop will provide an introduction to Cytoscape apps, which add functionality to the core software. It will focus on a specific app example, MetScape, which is used to visualize and interpret metabolomics and gene expression data in the context of human metabolic networks. A brief introduction to other apps, such as MCODE (cluster finding tool), SocialNetwork (builds co-publication networks), and MetDisease (annotates metabolic networks with MeSH disease terms) will be included.
Date & Time: 1:30pm - 4:00pm, Thursday, March 3, 2016
Location: C-103 - SHM 333 Cedar St, New Haven CT 06520
Presenter: Marci Brandeburg, University of Michigan
BioMart: A Research Data Management Tool for the Biomedical Sciences
Description: Some complex biomedical questions cannot be answered by reading the published literature. These may require aggregation of data from several data sets. In this regard, BioMart (www.biomart.org) is a freely available open source system that allows complex queries across more than 40 different biological data sets through a single web interface. Originally developed for the Ensembl genome browser, BioMart has been integrated into widely used software such as Galaxy, BioConductor, and Cytoskape. The BioMart interface is also used by data portals such as Ensembl, Wormbase, Gramene, and Reactome.
In this workshop we will use simple examples to demonstrate how to navigate, build queries, and save and export the results on BioMart such as:
- how to retrieve the Ensembl mouse genes and genomic locations in the first 10 Mbp of chromosome 1 region;
- retrieving 1 kb of upstream sequences from a cluster of human genes identified by an expression profile experiment;
- obtain a list of the SNPs that have been associated with RB1. For the SNPs, obtain several attributes such as source, rs ID, chromosome location, and pathogenicity
Date & Time: 12:00pm - 1:30pm, Thursday, March 10, 2016
Location: Medical Library, Simbonis Large Conference Room 101A, 333 Cedar St, New Haven CT 06520
Presenter: Rolando Milian
Novel Online Tools for Mining the Biomedical Literature
The rapid growth of experimental and computational biomedical data is being accompanied by an increase in the number of biomedical publications discussing these results. This makes retrieving relevant scientific information and identifying connections between findings, a challenging task. New literature-mining tools that make use of Natural Language Processing Algorithms and data visualization (e.g. CoreMine, NextBio, Semantic MEDLINE, etc) may be of help when sorting through this abundance of literature as discovery and hypothesis generating tools. This workshop provides an introduction on how to use some of these literature-mining tools when answering research questions and generating/narrowing hypothesis.
Date: Thursday, March 24, 2016
Time: 12:00pm - 1:30pm
Location: Cushing/Whitney Medical Library at Yale University, Simbonis Conference Room 101A, 333 Cedar St, New
Presenter: Rolando Milian
My Bibliography and SciENcv: grant reporting, compliance and biosketch through MyNCBI
Description: Although not required at this point, the NIH suggest the use of the Science Experts Network Curriculum Vitae (SciENcv), -a MyNCBI online tool- that serves as an interagency system designed to create biosketches for multiple federal agencies. This, along with the use of My Bibliography for grant activity reporting and NIH Public Access Policy compliance, increases the importance using MyNCBI as a tool for managing NIH-sponsored research. This workshop introduce researchers, research assistants and administrators on the effective use of these online tools and will cover the following among other topics:
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
How to use SciENcv to create different biosketches (from scratch, from external source, etc)
How to create and ORCID ID* and how to link SciENcv to that ORCID ID
*ORCID stands for Open Research and Contribution ID. Some publishers and journals (Springer, Wiley, Journal of Neuroscience, The Journal of Immunology, etc.) are asking authors to submit their ORCD ID along with their manuscripts for publication.
Date & Time: 12:00pm - 1:00pm, Thursday, April 21, 2016
Location: Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520
Presenter: Rolando Milian
