GSoC'17 Final Report

Final Work Product of NRNB DV-IMPACT

So we've officially come to an end to the amazing 12 weeks of Google Summer of Code 2017! This page summarize my entire work over the past 12 weeks.

Project Details

Project Title: Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) Database
Link to GSoC Project: https://summerofcode.withgoogle.com/projects/#6498470333513728
Open source Platform Used: Github
Organization Name: National Resource for Network Biology (NRNB)
Repository Contributed to: CANVD | PRMHAL
Mentor Name: Mohamed Helmy [helmy.sfc@gmail.com]

Code Links

Lint to all commits:
The DV-IMPACT Project The Peptide Recognition Module Database Project

Work Details

Phase I
  • Code Refactoring to improve Performance and Readability
  • Remove Unnecessary files from the project
  • Revamping the UI of the application
  • Remove inline CSS and JavaScript code
  • Fix several bugs present in the project
Phase II
  • Add support for file upload
  • Add support for file deletion
  • Add 'Search-and-Delete' feature for uploaded files
Phase III
  • Database modifications to handle PSI file
  • Add support for PSI file upload
  • Implement a progress-meter for backend file operation
Phase IV
  • Modify /variants and /network section based on schema changes
  • Add download support for PSI file
  • Make /dataset section dynamic + Add 'Search-filter'
  • Make /dataset editable by administrator
Phase V
  • Developing the Peptide Recognition Module Database Application
  • Developing the Admin Panel for PRM application
  • Developing the Network Visualization Module

An important part of my work include creation of a PSI format file from the previous database. With 240,000 mutation data joined with other tables, the resultant PSI file would have ~1,000,000 rows with extremely large file size. I successfully managed to create the PSI file from the previous data. This was one of the most challenging part of my work.

Snapshots

Data File Search + Delete Dataset Search + Edit + Download PSIMI-TAB File Uploader File Uploader Peptide Search Peptide Results

That's all Folks! It was really great working with the NRNB throughout this summer and it was a really valuable experience for me. Although GSoC period may end, my involvement to FOSS won’t! :)