Fall Training Sessions on Bioinformatics at the Medical Library

6 September 2016 - 10:40pm by Rolando Garcia-Milian

The Yale Medical Library is offering a number of bioinformatics training session this Fall. These sessions are free and open to any Yale affiliate but registration is required due to limited seating.

Please contact Rolando.milian@yale.edu  for questions or comments.

 

Title: The VERY Basics of the Unix Command Line

Registration required: http://schedule.yale.edu/event/2800083

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.

Date: Thursday, October 6, 2016

Time: 10:00am - 12:00pm

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St

Campus: Medical School

 

Title: Introduction to Enrichment Analysis Tools

Registration required: http://schedule.yale.edu/event/1154118

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 free tools for enrichment analysis as well as those licensed by the Medical Library

Date: Thursday, September 8, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St. Campus: Medical School

 

Title: Making Sense of Genomic Variation: Part 1 SNP Annotation

Registration required: http://schedule.yale.edu/event/2794996

The specific combination of genetic variation in an individual defines not only the external appearance but also susceptibility to diseases, cancer, genetic disorders, drug response, etc. This explains the great interest in discovering and cataloging these variations and using them for disease association and functional studies, among others. In this session we will review the most popular databases and tools to annotate, analyze and visualize genetic variations. Some of the databases and tools that will be discussed are:

  • dbSNP
  • Online Mendelian Inheritance in Man a comprehensive, authoritative compendium of human genes and genetic phenotypes.
  • GWAS Catalog/PheGenI
  • EBI-Ensembl Variant Effect Predictor to annotate and determine the effect of variants on genes, transcripts, and protein sequence, as well as regulatory regions.
  • And more…

Date: Thursday, September 22, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Making Sense of Genomic Variation: Part 2 Structural Variants

Registration required: http://schedule.yale.edu/event/2795002

Structural variation encompasses diverse types of genomic variants including deletions, duplications, inversions, transpositions, translocations, among others. In many cases, determining whether a particular genetic variant is pathogenic or benign and its correlation with respect to a patient's disease phenotype is challenging.

In this session we use online resources and tools to find, retrieve, annotate, and visualize structural variants

  • NCBI’s database of genomic structural variants dbVar
  • Database ofDatabasE of Chromosomal Imbalance and Phenotype in Humans
  • Genomic Variants DGVa
  • UCSC and Ensembl genome browsers

Date: Thursday, October 6, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Introduction to Genome Browsers. Part 1 Ensembl

Registration required: http://schedule.yale.edu/event/2795004

Ensembl provides access to genomic information with a number of visualization tools. By using Ensembl researchers can download data directly (e.g., genomic sequences), visualize many types of data (e.g., structural, variation, regulatory) directly on a genome assembly. In this session will review the basic functionalities and navigation of Ensembl by using specific examples. We will also use BioMart interface to answer questions and retrieve data and information from databases without the need of having any programming expertise.

Date: Thursday, October 20, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St.

Campus: Medical School

 

Title: Understanding Research Impact

Registration required: http://schedule.yale.edu/event/2803327

Nowadays, it is not uncommon for employers, academic institutions, and funding agencies to ask for evidence of research impact before making important decisions, such as tenure promotions, academic honors, or grant awards. Therefore, it is important for researchers to understand what research impact is and what they can do to document, enhance, measure and present their research impact to those decision makers. This session introduces the core concepts of research impact, its deep roots and long tradition, the various quantitative metrics of impact, and an emerging practical framework for telling impact stories. This session also introduces how to publish and disseminate research work in ways that improve discoverability and therefore enhance impact.

Date: Thursday, November 10, 2016

Time: 10:30am - 11:30am

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St

Campus: Medical School

 

Title: My Bibliography and SciENcv: grant reporting, compliance and biosketch through MyNCBI

Registration required: http://schedule.yale.edu/event/2795006

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 introduces 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: Thursday, December 1, 2016

Time: 11:00am - 12:30pm

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St

Campus: Medical School

 

Title: The VERY Basics of the Unix Command Line

Registration required: http://schedule.yale.edu/event/2803929

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.

Date: Thursday, December 8, 2016

Time: 10:00am - 12:00pm

Location: Cushing/Whitney Medical Library, Room 103 TCC, 333 Cedar St.

Campus: Medical School

 

For a full list of training sessions including PubMed, EndNote, etc. , please visit the medical library calendar: http://library.medicine.yale.edu/classes