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.
[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.
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:
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:
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.