 |
|
- Name - Aditya Saini
- Project - GPML Support in Newt
- Mentors - Hasan Balcı , Martina Summer-Kutmon & Yihang Xin
- GitHub Repo - GPML -to- CX2
- Newt Repo Commits - Newt
The goal of this project is to add new functionalities to Newt to be able to create biological maps in GPML format from scratch or edit existing ones. This will provide users to have a web-based alternative to PathVisio where they can easily create/edit GPML maps from any computer with Internet access. The functionalities to be added will also include access to WikiPathways, easy identifier mapping and data visualization etc., as in PathVisio.
For the past 15-16 weeks, I have been working on adding a palette in Newt for GPML (Graphical Pathway Markup Language), aiming to enhance the tool's usability for pathway visualization and editing. Additionally, I am focusing on the GPML to CX2 converter, which involves converting GPML data structures into CX2 format to ensure compatibility with Cytoscape and other bioinformatics tools. This task is critical for enabling seamless integration and improved data exchange within the pathway analysis ecosystem.
- In-depth Knowledge of GPML and CX2: Gained a comprehensive understanding of the data models and structures of both formats.
- JavaScript Parsing and Transformation: Improved skills in parsing complex XML-based files and transforming them into JSON.
- Schema Mapping Techniques: Developed the ability to map attributes between differing data formats while maintaining data accuracy.
- Error Handling Strategies: Learned to manage edge cases effectively, ensuring robustness in the converter.
- Developed familiarity with biological visualization tools and databases such as Newt, Cytoscape, PathVisio, and WikiPathways.
- Edges connected to shapes are not currently being drawn.
- Shape types such as Arc and Brace are not yet supported.
- Convert the Code to a Web Service.
- Integration of the GPML converter into Newt to enable importing GPML diagrams.
As we move forward in the real world, there's always room for improvement in every line of code. I want to extend my sincere thanks to my mentors, the organization admins, and the community members for their continuous support and assistance throughout this project. It has been an exciting journey working with this wonderful community, and I’ve gained so much from the experience. I would also like to thank Google for providing this incredible opportunity. Keep pushing code! 😊
Thank you for reading.