GSoC:Bio images
Google Summer of Code 2011
- Student: Michal Koziarski
- Mentors: Raoul J.P. Bonnal, Francesco Strozzi
The goal of the project is to implement graphical functions into the BioRuby objects, which will allow biological data to be visualized and exported easily.
Data storage will be based on samtools' Datasets, with possibility of further extensions.
For visualization, we've chosen Rubyvis. [1] It will generate SVG output, with possibility of converting it to other formats. In case that Rubyvis won't be enough, our second choice is XRVG. [2]
As for testing, we've chosen the BDD approach.
Currently, there are two github pages for the project:
Visualization package at https://github.com/e-mka/bioruby-vis (with wiki at https://github.com/e-mka/bioruby-vis/wiki)
Image browser at https://github.com/e-mka/bioruby-vis-browser
These are only the most important milestones. For the full history, you can check https://github.com/e-mka/bioruby-vis/commits/master
2011-08-09: Image browser was separated from bio-vis and is now available at https://github.com/e-mka/bioruby-vis-browser
2011-07-25: Image browser was created
2011-07-05: Bio::Image::Scatterplot and Bio::Image::Timecourse created
2011-06-25: Bio::Image::Panel created
2011-06-18: Prototype Bio::Image::Maplot created
2011-06-12: Bio::Image::Heatmap created
2011-06-07: visualization methods added to Array class
2011-06-05: Bio::File::Jpg created
2011-06-03: Bio::File and Bio::File::Svg created, Bio::Image::Point created
2011-06-01: visualize method added to Bio module. It enables adding visualization methods with ease. Also, simple image displaying was enabled.
2011-05-30: Bio::Image::Line created
2011-05-24: Bio::Image::Bar created
2011-05-22: generic Bio::Image created
2011-05-19: github repository created at https://github.com/e-mka/bioruby-vis