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A common task in the workflows of genomic biologists is to locate and inspect regions in genome-aligned data that show variation in many samples or genes. This can be a heavily repetitive task, going back and forth between manually extracting or querying the data regions and inspecting their details in visualizations (such as multiple sequence alignments). Ultimately, this hinders biologists in the comprehensive exploration of their data.
The goal of this project is to design a visual recommender system that guides users to:
(1) compose rules (flags) for feature patterns of interest (e.g., EventPad [1] and IGVMotif Finder [2])
(2) place and visualize the flags within regions of interest
(3) reuse flags for similar data
Requirements:
* Experience with javascript programming and d3.js
* Self-motivated to learn (or ideally already familiar with) recommender systems and pattern mining techniques
Reach out to Astrid van den Brandt (a.v.d.brandt@tue.nl) if you are interested in this project.
References
[1] B. C. M. Cappers and J. J. van Wijk, "Exploring Multivariate Event Sequences Using Rules, Aggregations, and Selections," in IEEE Transactions on Visualization and Computer Graphics, vol. 24, no. 1, pp. 532-541, Jan. 2018, doi: 10.1109/TVCG.2017.2745278
[2] IGV Motif Finder https://software.broadinstitute.org/software/igv/motif_finder
Project: Visual Recommender System for Flagging Features of Interest in Large Genomic Alignments
Description
A common task in the workflows of genomic biologists is to locate and inspect regions in genome-aligned data that show variation in many samples or genes. This can be a heavily repetitive task, going back and forth between manually extracting or querying the data regions and inspecting their details in visualizations (such as multiple sequence alignments). Ultimately, this hinders biologists in the comprehensive exploration of their data.The goal of this project is to design a visual recommender system that guides users to:
(1) compose rules (flags) for feature patterns of interest (e.g., EventPad [1] and IGVMotif Finder [2])
(2) place and visualize the flags within regions of interest
(3) reuse flags for similar data
Requirements:
* Experience with javascript programming and d3.js
* Self-motivated to learn (or ideally already familiar with) recommender systems and pattern mining techniques
Reach out to Astrid van den Brandt (a.v.d.brandt@tue.nl) if you are interested in this project.
References
[1] B. C. M. Cappers and J. J. van Wijk, "Exploring Multivariate Event Sequences Using Rules, Aggregations, and Selections," in IEEE Transactions on Visualization and Computer Graphics, vol. 24, no. 1, pp. 532-541, Jan. 2018, doi: 10.1109/TVCG.2017.2745278
[2] IGV Motif Finder https://software.broadinstitute.org/software/igv/motif_finder
Details
- Supervisor
-
Huub van de Wetering
- Secondary supervisor
-
Astrid van den Brandt