Knowledgebase and Forums/Tutorials and Reference Materials

How-To Videos

Stephen Wilson
posted this on April 6, 2010, 1:05 PM

Below you'll find recordings of the 2014 and 2015 User Workshop presentations that address the features of the newly redesigned IEDB 3.0 production website and the epitope prediction and analysis tools in the Analysis Resource.  There are also short videos about the IEDB based on the IEDB 2.x legacy website that provide useful examples and explanations that can be applied in principle to the redesigned website.

Copies of the slide presentations for the 2014 and 2015 IEDB User Workshops can be found at http://help.iedb.org/forums/67092-Tutorials-and-Reference-Materials.

 

Introduction to the IEDB, Populating the database, Searching the IEDB for content

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IEDB Overview, data curation, and data structure

Overview of the IEDB resource (19 minutes)

IEDB data structure and curation (17 minutes)

Data query and reporting features

Finding Data Using the Home Page Search (29 minutes)

Finding Data Using the Specialized Searches (12 minutes)

The Immunome Browser (26 minutes)

Home page search examples (20 minutes)

Specialized search examples (20 minutes)

Four infectious disease related queries (23 minutes)

Two autoimmune disease related queries (15 minutes)

Finding T and B cell epitopes in a give protein of interest (5 minutes)

Example allergy query (3 minutes)

IEDB and cancer epitopes (2 minutes)

Queries and IEDB features relevant to vaccine development (2 minutes)

Help and support features; database export options (2014 user workshop) (25 minutes)

 

IEDB Analysis Resource - Epitope Prediction and Analysis Tools, including epitope visualization

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Introduction to the Analysis Resource (29 minutes)

MHC class I binding prediction tools (41 minutes)

MHC class I processing and immunogenicity tools (27 minutes)

MHC class II binding prediction tools and API, including TepiTool (62 minutes)

TepiTool - a wizard interface for predicting MHC class I and II binding (20 minutes)

B cell epitope prediction tools (67 minutes)

Homology mapping tool and Epitope Viewer (2014 user workshop) (23 minutes)

B Cell Epitope Modeling and Docking, including Prediction of ImmunolGlobulin Structure (PIGS) (10 minutes)

Analysis Tools (9 minutes)

Tool downloads, epitope prediction references and benchmarks, and how to contribute tools to the IEDB (4 minutes)

Paratome (prediction of antigen binding regions of antibodies), Benchmark references and data sets, tools download, and how to contribute tools to the IEDB Analysis Resource (2014 user workshop)  (9 minutes)

 

IEDB 2.x Legacy Website

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Overview of the IEDB

Introduction to the IEDB site and Search Options

Simple Search Overview

Searching the IEDB

Simple Search: Finding Epitopes from a Protein

Peptide/Protein Homology Search

Linear Sequence Queries

Advanced Search Overview

Advanced B cell search: Example of finding antibody cross-reaction

How do I generate a list of all proteins from which epitopes have been identified for an organism of interest?

Using the Disease Finder

Understanding Query Results

Results: Epitope Listing, Details of Individual Entries and Using the Export Function

 

 

 

 

 
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