cBioPortal Study View: Advanced Dashboard Integration

[dippindots]

Background

The current cBioPortal Study View primarily displays clinical and genomic data. We want to develop new features that extend this view by integrating:

• Spatial-oriented Dashboards: For studies with imaging data, these dashboards will highlight spatial features such as tumor-infiltrating lymphocytes (TILs) and spatial marker densities.
  
• Curated Study Dashboards: For specific studies, these dashboards will automatically display key research findings (e.g., gene expression differences), reproducing insights from research publications.
  

A sample study that can be used for development and testing is the crc_orion_2024 study.

Goal

Enhance the current cBioPortal Study View, which primarily displays clinical and genomic data, by incorporating new dashboard features that add both spatial visualizations and curated study-specific plots. This enhancement is designed to:

• Enrich the user experience by adding spatial data insights to the existing clinical and genomic data.
• Automatically configure dashboards based on study metadata, ensuring that key findings and spatial features are prominently displayed.

Approach

1. Design and Layout:

   • Create a default spatial-oriented dashboard layout that emphasizes critical spatial data (e.g., TILs and cell density).
   • Develop a configuration system to detect studies that require curated dashboards and predefine the visualizations to be displayed.

2. Backend & Frontend Integration:

   • Enhance backend services to process study metadata and automatically select the appropriate dashboard configuration.
   • Update frontend components to dynamically render both spatial visualizations and curated study-specific plots, ensuring a seamless integration with the current clinical and genomic views.
   • Address challenges such as summarizing data from multiple samples, similar to the approach used in the structural variants table within Chromoscope.

3. Testing and Validation:

   • Conduct thorough testing across various study types to ensure that the new dashboards accurately display the intended data.
   • Collect feedback from users and domain experts to refine the dashboard design and functionality.

Needed Skills

• Full-Stack Development: Experience with backend technologies (e.g., Java/Spring) and modern frontend frameworks (e.g., React, Angular).
• Data Visualization: Proficiency with visualization libraries and tools for handling spatial data and study-specific plots.

Possible Mentors

Gaofei (@dippindots)
Ino (@inodb)
Bryan (@gblaih)

[Dheerajr444]

Hi everyone, @dippindots
I'm Dheeraj interested in working on this project as part of GSOC. I'm new to frontend development, but I'm eager to learn and contribute to this project. Could you please provide any additional details or guidance on how to get started? Also, let me know if there's anything specific you'd like me to focus on.

Looking forward to contributing!

[psyee09]

Hello everyone, @dippindots

I am Saee, and I am currently majoring in Biomedical Engineering from ASU additionally minoring in statistics. I am new to data visualization processes (mostly R, python and Excel) and have been getting an hands-on on the same as a part of my coursework as well as my research project this semester, but I would love to know more about the same as a part of GSoC.

Any additional information about getting more involved would be appreciated andI cannot wait to know more about the project!

[ndhaliwal59]

Hello everyone.

I'm a Computer Science student really into full stack and data visualization. I also completed the Google Data Analytics Certificate, which gave me some experience in working with structured data and drawing insights from it.

I think it's exciting to see how spatial visualization will be integrated with clinical and genomic data in this project because I would like to contribute and understand how backend and frontend components will synchronize for dynamic dashboard rendering.

Could we schedule a quick Zoom call to discuss the project a bit further? I would love to hear more about the expected workflows and how I can best contribute. Look forward to hearing your thoughts!

Best,
Nishan

[KaifScripts]

Hello all, @dippindots

My name is Kaif, a Computer Science major looking forward to working on this project under GSoC. Following my analysis of the codebase of cBioPortal.
For the frontend, utilizing React (TypeScript) with Recharts, Vega-Lite, Leaflet.js, and Deck.gl for interactive visualizations. A dynamic layout system for the dashboard could be implemented, automatically setting up study-specific plots through GraphQL APIs (Apollo Client).

For the backend, I will enhance the Spring Boot (Java) GraphQL API to retrieve and process spatial metadata, query optimization via PostgreSQL (PostGIS). A configuration engine will auto-detect spatial features and recommend applicable plots.

In order to manage large amounts of data effectively, lazy loading, tile-based rendering, and data aggregation methods will be utilized. Testing will be done with Jest, React Testing Library, JUnit, and Mockito, and validation through the crc_orion_2024 study.

Looking forward to collaborating, sharpening this methodology through feedback, and working together to enhance the cBioPortal experience. Can't wait to hear your input!

[KhushalGupta]

Hello All,
I am a full-stack developer with a strong background in both backend and frontend technologies, making me well-suited to tackle the challenges of enhancing the cBioPortal Study View. I have experience in working with large datasets, integrating complex visualizations, and ensuring seamless integration between different layers of a system. I would be available for 20-30 hours/week.
I have good experience with Angular and Spring Boot and also integrating Tests and Github Actions CI/ CD. My skill set aligns perfectly with the goals of this project, particularly in the areas of data visualization, backend development, and frontend integration.
Critical points to implement here:- are Lazy Loading, Virtual Scroll for dropdown for large DataSets, refreshing of UI based on filters, batch queries for performance, scrolling for visualizations components, caching of the data whenever needed and reduced application first load times and ofcourse keeping in mind the CSP and accessibility issues.
Thanks.

[aaki25]

Hey everyone, @dippindots

My name is Aakarshit, I am a full stack developer with 2 years experience in React, Node, Django. I know Java as well and I am looking forward to learning more via working on this project. I'll be available for 30 hours/week.
Thank you.

[aaki25]

Hey everyone, @dippindots

My name is Aakarshit, I am a full stack developer with experience in React, Node, Django. I know Java as well and I am looking forward to learning more via working on this project and I hope I could get my first opensource experience through this project. I'll be available for 30 hours/week.
Thank you.

[mallikaakash]

Hello, everyone, @dippindots
My name is Aakash Mallik and I am a Final year undergraduate at the National Institute of Technology Karnataka, Surathkal. am currently majoring in Electrical and Electronics Engineering, and hold a minor specialization in Computer Science Engineering.

I have previously worked as a research intern at premier institutes like IISc and IIT Delhi. At IIT Delhi my work involved working on medical data to create an initial protoype model for the prediction of progressionof Non-Alcoholic Fatty Liver Disease(NAFLD), under Dr. Tapan K Gandhi.

Apart from this I have worked at 4x startups. My recent work includes being an AI researcher and developer at an AI wearable startup, Neosapien. Over here we build smart pendants that serve as an assistant and extension to your memory. I have also freelanced as a web-developer.

Thank you for your time.

Cheers.

[ssharan3]

Hi Team,

I am interested in contributing to this idea. I have good experience in .net and react. Interested in working on this project.

Looking forward to contribute.

[rushipatilGit]

Hi Gaofei ,

Myself Rushieksh, I have close to 15+ years of experience in development, implementation, consulting of software projects, passion for technology and problem-solving,I would love to contribute towrds Open Source project , well versed with technologies such as JAVA, J2EE, Spring Framework,Spring Boot 3.X, Hibernate, Spring Data JPA,Spring Security,JMS, Rest API, Ant/Maven/Gradle as build tools, MS SQL, AWS,GCP & Azure cloud technologies.

I am always eager to learn and adapt to new technologies and methodologies, would love to contribute towrds this exciting Open Source Project.
Please drop me a email at rp150982@gmail.com , eager to hear from you.

Thanks,
Rushikesh.