search

nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
116 stars 39 forks source link

Experiment data overlay in Newt #138

Closed ugurdogrusoz closed 4 years ago

ugurdogrusoz commented 4 years ago

Newt is a Cytoscape.js based viewer and editor for biological maps in Systems Biology Graphical Notation (SBGN) notation [1] 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 [2]. 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] 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.

Goal

With this project, we aim to design and implement experiment data overlay support for the Newt editor. We will probably use a simple tab-delimited text format to upload experiment data from. Multiple data sets should be supported as well. The user should be able to customize what is to be shown and how.

Difficulty Level 2

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 (essential) SBGNViz and ChiSE (nice to have)

Public Repository

Newt GitHub repository

Potential Mentors

Ugur Dogrusoz

Contact

Ugur Dogrusoz

aditya20t commented 4 years ago

Hello, I am interested in this project. Can I take this project?

ugurdogrusoz commented 4 years ago

@adad20 if you qualify (and NRNB is selected as an organization to participate this yera), you may write a proposal on this or other project ideas. Procedure is detailed here and in GSoC web pages.

aditya20t commented 4 years ago

okay

aditya20t commented 4 years ago

@ugurdogrusoz Is there anything to get started before the proposal period. I want to know more about the organisation and project.

ugurdogrusoz commented 4 years ago

@adad20 Looks like we will remove this from project ideas since there's been a lot of progress on this module already, sorry.

aditya20t commented 4 years ago

@ugurdogrusoz No problem I will look at the other projects.