Interactive Web-Overlay for Biochemical Pathway Exploration

Type: 
BA/PR
Persons: 
1

Description

Biologists refer to biochemical pathways to explore series of chemical reactions occurring within an organism. Overview or partial visualizations, such as the KEGG reference pathways, are well-known representations for biologists, and are useful for comparing the function of individual enzymes in a larger context. However, these visualizations are mainly used as static snapshots of biochemical pathways and the existing web services offer little support for complex queries or visual comparisons using familiar representations. Moreover, new combinations resulting from the recruitment of existing genes to different pathways can only be manually represented.

Tasks

The goal of this work is to design, develop, and validate an interactive web overlay for visually comparing the function of different biological entities on top of the familiar KEGG reference pathway visualization. The KEGG API can be used to link individual reactions, enzymes, or genes to compounds and orthologs, which are the building blocks of the KEGG reference pathway. The main objective is to visualize the query results as interactively explorable overlay on top of the existing KEGG pathway visualizations within a standard web browser.

Requirements

  • Strong interest in information visualization and the biology domain
  • Programming experience
  • Experience with web technologies (JavaScript, d3, …) advantageous
  • Biological knowledge advantageous
  • Commitment to collaborate with experts from the biology domain in an interdisciplinary way

Environment

The work should facilitate interactive exploration of the existing KEGG reference pathway within a standard web browser. The suggested environment is a Chrome extension. However, based on prior experiences of the student, alternative environments can also be considered. 

This work will be done in collaboration with the Genome Evolution and Ecology group of the Faculty of Life Sciences at Universität Wien.

Contact

For more information please contact Manuela Waldner (waldner@cg.tuwien.ac.at).