Local DB support for SBGN maps in Newt

ugurdogrusoz commented 3 years ago

Background

Newt [1] is a Cytoscape.js based viewer and editor for biological maps in Systems Biology Graphical Notation (SBGN) notation [2] to create biological maps from scratch or edit existing ones. It's been built (with partial support from GSoC) around an editing library named ChiSE, which in turn was based on a viewer library named SBGNViz [3]. The tool uses a number of new Cytoscape.js extensions built for various editing capabilities such as grid-guidelines, context-menus, and expand-collapse.

[1] H. Balci et al., "Newt: a comprehensive web-based tool for viewing, constructing, and analyzing biological maps", Bioinformatics, to appear.

[2] M. Sari et al., "SBGNViz: a tool for visualization and complexity management of SBGN process description maps", PLoS ONE, 10(6), e0128985, 2015.

[3] N. Le Novère et al., "The Systems Biology Graphical Notation", Nature Biotechnology, 27, pp. 735-741, 2009.

Goal

The goal of this project is to integrate local database support for Newt to store SBGN maps on a shared server. We would like these maps to be integrated as they are deposited into the database. We would also like to see a rich set of queries to properly access the maps of interest based a genes of interest of the user using graph based queries such as those provided in [4].

A graph database Neo4j would probably be a good choice of technology for this purpose.

[4] U. Dogrusoz et al., "Algorithms for Effective Querying of Compound Graph-Based Pathway Databases", BMC Bioinformatics, 10:376, 2009.

Difficulty Level 3

The project can be considered a fairly difficult one since it involves work in back end and front end programming.

Skills

HTML, JavaScript, Cytoscape.js and its extension structure, and Neo4j (essential) SBGNViz and ChiSE (nice to have)

y-pankaj commented 3 years ago

Hi @ugurdogrusoz, Pankaj here, a senior undergraduate from India. I found this project interesting and it aligns with my tech stack as well, so I would like to work on this project. I have mailed you my resume and certain queries that I had. Hoping to hear back from you soon!

ugurdogrusoz commented 3 years ago

Responded through email.

khanspers commented 3 years ago

This is an active GSoC 2021 project. The issue will be closed for the duration of GSoC since it is no longer available to other students.

nrnb / GoogleSummerOfCode