Improvements in tool for curating biological maps in SBGN

[ugurdogrusoz]

Background

SBGNViz [1] is a Cytoscape.js based viewer for biological maps in Systems Biology Graphical Notation (SBGN) notation [2]. ChiSE is based on SBGNViz to add editing facilities for construction of SBGN maps or modification of existing ones.

Goal

ChiSE already supports many features including:

• SBGN PD notation
• expand-collapse and hide-show for complexity management of large maps
• layout support
• undo/redo, grid and grid guidelines support

With this project, we aim to design and implement new features for the ChiSE editor.

Description

Among the new features that are scheduled for the first public availability are:

• support for Activity Flow notation and multiple node/edge palletes
• user profiles
• port / connection point support
• user interface improvements
• miscellaneous other features

Difficulty level: 2

This project requires good programming skills. Experience in web technologies (JavaScirpt , html, css) is required. Experience with Cytoscape.js and its extensions is a plus.

Potential mentors

Alexander Mazein, Ugur Dogrusoz

[1] M. Sari, I. Bahceci, U. Dogrusoz, S.O. Sumer, B.A. Aksoy, O. Babur, E. Demir, "SBGNViz: a tool for visualization and complexity management of SBGN process description maps", PLoS ONE, 10(6), e0128985, 2015.

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

[kinimesi]

Hi, I have submitted the draft of my proposal. Could you please review it and give feedback? Thanks. @ugurdogrusoz @amazein

[khanspers]

GSoC 2017 selected project