Background & design philosophy
The Next-Generation (NXG) IEDB Tools site (NXGT, for short) 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 take advantage of the new functionalities to perform complex workflows.
NXGT is a complete redesign of the IEDB Tools site and contains many new features that are impactful. Some of the most notable features are briefly described here and described in detail elsewhere.
The user interface has been completely reimagined with the goal of removing clutter and presenting users only with critical inputs. For instance, it is possible to run a MHC class I binding prediction after entering/pasting a sequence into the ‘Input Sequence’ box and clicking the ‘Run’ button. All other parameters, including the binding prediction algorithm, 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.
Building upon the integration of related tools, we have also added the capability to use the output of one tool as input for another, in order to build up data processing pipelines. For instance, starting with a set of protein sequences, a user can predict for MHC binding, immunogenicity, and processing, filter their results and send the resulting sequences 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 and we believe they will become an integral part of every NXGT user’s workflow.