GSoC:Bio images

Naohisa Goto edited this page Jun 14, 2016 · 1 revision

Represent bio-objects and related information with images

Google Summer of Code 2011

  • Student: Michal Koziarski
  • Mentors: Raoul J.P. Bonnal, Francesco Strozzi

Description

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.

Github

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

Sample Graphical Output

SampleBar.jpg

SampleLine.jpg

SamplePoint.jpg

SampleHeatmap.jpg

Bio-vis-browser

Bio-vis-browser.png

GSoC Progress

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

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