IEDB Solutions Center

Stephen Wilson October 08, 2008 General Announcements and Updates

Welcome to the Solutions Center. Here you can submit a help request using the New option in the menu above, or you can search or browse our Knowledge Base and Forums (on the right). If you register, you can track your help requests and post topics to the Forums.

User Documentation is available here.

Video Tutorials are available here.

Other tutorial and reference material is available here.

If you have a general question or comment and don't want to post it in the forums, you should feel free to email us at help@iedb.org

Ward Fleri Oct 07 Tutorials and Reference Materials

The slide presentations from the 2014 IEDB User Workshop are available below as pdf files.  The webcast sessions can be viewed in the How-to Videos folder.

Schedule

Day 1 Presentations

  1. IEDB Overview (2-IEDB_Overview2014Day1.pdf)
  2. The Data (3-Data2014Day1.pdf)
  3. Finding data in the IEDB (4-Query2014Day1.pdf)
  4. Immunome Browser (5-ImmBrowser2014Day1.pdf)
  5. Query examples (6-Examples2014Day1.pdf)
  6. Support and help features; exporting data (7-Support2014Day1.pdf)

Day 2 Presentations

  1. Analysis Resource introduction (1-AnalysisResourceIntro2014Day2.pdf)
  2. MHC class I binding predictions (2-classI2014Day2.pdf)
  3. MHC class II binding predictions; RESTful interface (3-classII2014Day2.pdf)
  4. T cell processing prediction, immunogenicity, and analysis tools (4-classI_processing2014Day2.pdf)
  5. B cell epitope prediction tools (5A-BcellPred2014Day2.pdf)
  6. Homology Mapping tool (5B-HomologyMapping2014Day2.pdf)
  7. EpitopeViewer (5C-EpitopeViewer2014Day2.pdf)
  8. PIGS (5D-PIGS2014Day2.pdf)
  9. Paratome, epitope prediction benchmark references and data sets, and tools download (6-Paratome_et_al2014Day2.pdf)

Randi Vita Aug 12 General Announcements and Updates

The IEDB 3.0 site is currently publicly available as an beta site (http://www.iedb.org/beta) and is on target to be released by the end of
the summer 2014. This newly designed interface includes new search functionality, including the ability to filter query results on the fly and added search parameters. 

Special Features

  • Most commonly used search parameters moved to center of the home page
  • Epitope Analysis Resource tools made more prominent and easier to find on homepage
  • New results page has left hand search panel to allow filters to be added to the existing result set on the fly
  • Results can be quickly revised using either the "Reset" button or by selectively removing each filter
  • Completely new ‘Antigen’ table organizes and presents epitope data by its antigen
  • Epitope table now provides the numbers of references and assays describing each epitope
  • Immunome Browser now integrated into results tables
  • Ability to limit query results by specific assay type available on results page

 

Please check out the new beta site http://www.iedb.org/beta and provide feedback.

 

Stephen Wilson April 06, 2010 Tutorials and Reference Materials

Below you'll find short videos about the IEDB that feature actual screen animations and voice overs from IEDB curators.  There are also recordings of the 2013 User Workshop presentations on the Analysis Resource.  These are longer in length.  Please note that the volume of the audio does fluctuate.  These videos are listed in the order they were presented on 2 October 2013.

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

Using the Organism Finder

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

2014 User Workshop Webcasts

Overview of the IEDB resource, presented by Dr. Bjoern Peters (19 minutes)

IEDB data structure and curation, presented by Dr. Randi Vita (17 minutes)

Finding Data in IEDB 3.0, presented by Dr. Kerrie Vaughan and Nima Salimi (51 minutes)

The Immunome Browser, presented by Drs. Julia Ponomarenko and Kerrie Vaughan (40 minutes)

Query examples, presented by Dr. Kerrie Vaughan and Nima Salimi (28 minutes)

More query examples, presented by Dr. Kerrie Vaughan and Nima Salimi (86 minutes)

Help and support features; database export options, presented by Dr. Deborah Shackelford (25 minutes)

Introduction to the Analysis Resource, presented by Dr. Bjoern Peters (22 minutes)

MHC class I binding prediction tools, presented by Dr. Edita Karosiene (41 minutes)

MHC class II binding prediction tools and API, presented by Dr. Sinu Paul (50 minutes)

MHC class I processing and immunogenicity tools, presented by Dr. Bjoern Peters (27 minutes)

B cell epitope prediction tools, presented by Dr. Julia Ponomarenko (59 minutes)

Homology mapping tool and Epitope Viewer, presented by Dr. Julia Ponomarenko (23 minutes)

Prediction of ImmunolGlobulin Structure (PIGS), presented by Dr. Julia Ponomarenko (18 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, presented by Dr. Bjoern Peters (9 minutes)

 

 

 

 

Stephen Wilson January 21, 2009 Tutorials and Reference Materials

The attached PDF file includes documentation of IEDB Version 2.0.  It contains instructions and graphical examples of the IEDB user interface.  Below is an introductory paragraph.

 

Introduction
The Immune Epitope Database and Analysis Resource (IEDB) is a public repository of immune epitope data and is sponsored by the National Institute for Allergy and Infectious Diseases (NIAID).  The IEDB development started in December 2003 and it became available to the public in a beta test phase on 15 February 2006.  The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.  The IEDB also makes available a variety of analytical and epitope prediction tools and resources within its Analysis Resource.  Since its initial release, the IEDB functionality has been incrementally improved and enhanced.  A major redesign of the underlying data schema and the web interface was released in January 2009 and was designated IEDB 2.0.  Several updates have been deployed since that time.  This document described the features of IEDB Release 2.9 as of August 2010.