Extending and improving PathVisio data import

Background

PathVisio is a pathway editor and analysis tool. PathVisio allows users to upload and visualize data on biological pathways. Currently, it is possible to upload only one dataset at a time as a comma separated file. This process needs to become more user-friendly and flexible. Check out the PathVisio data visualization tutorial on how the data import works at the moment.

Features:

Loading multiple datasets at once: these could be any kind of quantitative or qualitative data about any pathway element, such as genes, proteins, metabolites, and interactions.
Linking each individual dataset to a particular element on a pathway, for eg. linking a gene expression dataset to genes on pathways and a flux data set to interactions on pathways.
Importing data from multiple file formats (For eg: .xls, .ods).
Create a pop-up panel accessible from the menu bar of the PathVisio main window to show (1) all the currently loaded datasets, (2) the biological elements they are linked to, and (3) the currently loaded annotation databases.

Goal

This functionality should be extended to allow uploading a number of data files at the same time as well as uploading of multiple data file formats (for eg. Excel sheets) should be allowed. This will involve extending the gex and data modules of PathVisio. These modules are part of the PathVisio core and take care of importing experimental data and mapping it to the elements in a pathway.

Difficulty Level 2

Changes in the core part of the application.

Skills

Java (essential)

nrnb / GoogleSummerOfCode