Organization - Open Bioinformatics Foundation (OBF)
- Name - Haputhantrige Chalith Tharuka Gunasekara
- Email - [email protected]
- GitHub Profile - https://github.com/chaliya96
- LinkedIn - https://www.linkedin.com/in/chaliththaruka12/
Analyzing positional features/annotations in sequences is important in bioinformatics. Visualizing such data is quite a challenging task, considering the large amount of data to be displayed. The feature viewer is an open source javascript library developed to visualize biological data (referred to as features) mapped to a linear sequence (Paladin et al., 2020). For instance, it can be configured to visualize the location of protein domains or amino acid variations in a protein sequence. The feature viewer is being used in several popular bioinformatics resources such as neXtProt and COSMIC 3D.
Currently, the feature viewer supports limited configurability options in the features displayed, such as the color, shape and on-click behavior. This is too restrictive for some of the possible use cases of the feature viewer, where more flexibility is required in the display of features. One such instance is when different types of amino acid variants should be displayed in a color-specific manner in the same feature track.
The overall goal of this project is to improve the configurability of the feature viewer, such that it allows greater flexibility in the visualization of detailed biological data.
Through this implementation, feature-viwer got a new chart type of BAR. The main reason for implementing this chart type is to represent numerical values such as frequency in a separate manner.
| Pull Requests | Status |
|---|---|
| calipho-sib/feature-viewer#67 | Merged |
When the developer needs to highlight a specific part of very long features with large amounts of data, this implementation can be used. The developer can add different colors, shapes or text according to the requirements.
| Pull Requests | Status |
|---|---|
| calipho-sib/feature-viewer#69 | Merged |
| calipho-sib/feature-viewer#72 | Merged |
This feature can be used to load data to feature-viewer on demand. Before this for all the features defined, the feature viewer fetches data from the respective backend API in its initial load. For features with large size of data, this was taking very long time and there was no option to prevent this even the user does not want all the data. Using this feature now developers can set summary view in initial view and get the required data only when user requests.
| Pull Requests | Status |
|---|---|
| calipho-sib/feature-viewer#69 | Merged |
Through this implementation the users will be able to download the contents as svg format.
| Pull Requests | Status |
|---|---|
| calipho-sib/feature-viewer#76 | Work In Progress |
Feature Viewer documentation is updated with realted to added new features, their properties and options. New examples also added with addtional information.
| Pull Requests | Status |
|---|---|
| calipho-sib/feature-viewer#75 | Merged |
- v1.3.0-beta.1 - https://github.com/calipho-sib/feature-viewer/releases/tag/v1.3.0-beta.1
- 1.3.0-beta.3 - https://github.com/calipho-sib/feature-viewer/releases/tag/1.3.0-beta.3
I will always be grateful to to my mentors - Kasun Samarasinghe, Lydie Lane, nextProt team and OBF for their guidance and constant supervision as well as for providing necessary information regarding the project.