search

nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
114 stars 38 forks source link

Web based SBGN editor #60

Closed ugurdogrusoz closed 8 years ago

ugurdogrusoz commented 8 years ago

Background

SBGNViz.js, or simply SBGNViz, is a software tool / library for viewing process description maps in Systems Biology Graphical Notation (SBGN-PD) [1]. It is based on Cytoscape.js. A sample application for the library is provided here.

Goal

With this project, we aim to turn SBGNViz into a full-blown editor/curator tool for biologists to construct new models or modify existing ones in SBGN-PD notation.

Description

Currently SBGNViz allows one to load process description maps in SBGN-ML format and apply certain filtering operations but it doesn't allow you to modify the topology of the maps. This project aims adding new facilities for adding / removing biological entities and processes of varying types into / from a new map or an existing one. In addition, operations for resizing and annotating (with state variables and units of information) biological entities are to be provided. Furthermore, advanced complexity management techniques including expand/collapse of complexes and compartments and corresponding specialized layout operations are to be employed. Finally undo/redo support is needed to recover from mistaken operations.

Potential Mentors

Ugur Dogrusoz, Ozgun Babur

[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.

stefan2212 commented 8 years ago

Hello :) . My name is Stefan and i study Computer Science at University Alexandru Ioan Cuza from Iasi Romania. I am in the second year of study and i would like to participate at this project

ugurdogrusoz commented 8 years ago

Please take a look at this paper to learn about SBGNViz.js. This is what we'd like to turn into a full pledged editor. So far, we have done quite a bit of work. Latest can be found here: http://cs.bilkent.edu.tr/~ivis/SBGNViz.js_editor/sample-app/

This project aims to improve the editing capabilities of the tool further with things like specialized layout upon expand/collapse, creation of processes through templates provided to the users, etc.

khanspers commented 8 years ago

Chosen as GSoC 2016 project.