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Published on: August 15, 2019
The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.
Steve Fischer1, Cristina Aurrecoechea, Brian P Brunk
1Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA. sfischer@pcbi.upenn.edu
Summary
The Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) launched the Strategies WDK, a user-friendly interface for complex data analysis. This tool simplifies searching and data set operations for researchers studying eukaryotic pathogens.
Area of Science:
- Bioinformatics
- Computational Biology
- Parasitology
Background:
- The Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) provides access to extensive data for eukaryotic pathogens.
- Advanced data analysis and exploration of relationships across datasets are crucial for identifying therapeutic targets and understanding pathogen biology.
- Existing interfaces may present challenges for users needing to perform complex set and interval operations on biological data.
Purpose of the Study:
- To introduce the Strategies WDK, a new graphical user interface designed to simplify advanced data searching and manipulation for EuPathDB users.
- To enable researchers to easily perform dynamic computational experiments and explore complex relationships within biological datasets.
- To facilitate the identification of novel therapeutic targets by allowing researchers to pinpoint specific pathogen characteristics.
Main Methods:
- Development of a graphical user interface (GUI) based on usability studies.
- Implementation of a strategy-based workflow allowing users to chain searches using set and genomic interval operators.
- Integration of a visual display (Venn diagrams) to illustrate the logic of user-defined strategies.
- Deployment of the Strategies WDK across all EuPathDB databases and other projects.
Main Results:
- The Strategies WDK provides an accessible platform for advanced searching and data set operations.
- Researchers can easily construct and modify complex data analysis strategies.
- Strategies can be saved as shareable protocols, promoting reproducibility and collaboration.
- The system is compatible with various genomics and biological warehouse databases.
Conclusions:
- The Strategies WDK significantly enhances the usability of EuPathDB resources for complex data analysis.
- The tool empowers researchers to conduct sophisticated computational experiments, accelerating discovery in eukaryotic pathogen research.
- The flexible architecture and availability for download promote wider adoption and application in the field.
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