General Site Usage and Specific Tools
In-depth documentation for the Next-Generation (NG) IEDB Tools site, or NGT, as well as documentation for using specific tools, can be accessed here: https://nextgen-tools.iedb.org/docs/. The article below provides a brief overview of the new site.
Background & Design Philosophy
The Next-Generation (NG) IEDB Tools site (NGT) provides a completely new user interface for epitope prediction and analysis tools. The main goals of the redesign were to:
- simplify the user experience
- enhance existing functionality
- add new functionality
- ensure consistency among the tools
- improve the layout and aesthetics
The interface should allow new users to feel comfortable and have an immediate understanding of how to get started using the website. At the same time, power users should be able to leverage the new features to carry out complex workflows.
Notable Features
The NGT is a complete redesign of the IEDB Tools site and contains many impactful new features. Some of the most notable features are briefly described as follows.
Minimalistic Interface
The user interface has been completely reimagined to remove clutter and present users only with critical inputs.
For instance, it is now possible to run a MHC class I binding (MHC-I) prediction just by providing a sequence. All other parameters (prediction models, peptide lengths, and alleles) are set to defaults to allow users to get right to work.
Once the tabular results appear, users can go back and make adjustments to these parameters to generate a more targeted result. We envision the tools to be used in an iterative manner like this.
Integration of Related Tools
In the NGT, we have attempted to group related prediction tools into a single application.
For instance, all tools related to MHC-I binding, MHC-I processing, and MHC-I immunogenicity have been bundled into the T cell class I application.
This allows users to run multiple predictors against one input dataset and receive the results in a single comprehensive table.
Pipelines
Building upon the integration of related tools, we have built data-processing pipelines that use the output of one tool as input for another.
For instance, starting with a set of protein sequences, a user can run a T Cell Class I prediction that includes MHC binding, immunogenicity, and processing. The user can then filter their results and send them to the Clustering tool to remove redundancy. The clusters can then be sent along to Pepmatch to identify closely related sequences in a different species.
Pipelines are designed to be extensible, reusable, and shareable.
We believe they will become an integral part of every NGT user’s workflow.