Prince:Open Computing Projects

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These are for peripherally related projects that may help your main work, although they might become a full-blown project in their own right. Have an interesting project idea? Something that would help your work? List it here. If you are working on one of these put your name by it so others can talk to you about it.

General

  • Cloneable WIKI based on git: Develop a wiki that uses markdown for the front-end and git (preferably abstracted) for the backend.
    • Should be extremely easy to use, organize, clone, share, etc.
    • File structure should be easily navigable within the repository and on the web interface.
    • Seems like a candidate: git_store
  • Any of the projects on Ruby Bounties

Numeric Computing

  • NArray in Inline: Figure out how to manipulate NArray objects from within Inline
  • Implement NArray completely within FFI (and/or FFI-Inliner).
  • NArray Tutorial: Create a tutorial for NArray based on the methods page
  • NArray <=> NumPy Equivalency: Create a NumPy equivalency document showing how to do things in NArray and NumPy.
    • This could be based on the NumPy User Guide and/or Reference
    • Extend NArray as necessary so that all useful functionality of NumPy is duplicated in NArray or separate gems.

Visualization

**NOTE**One alternative may be the sfdp algorithm implemented in graphviz. (pdf describing the technique).

LGL creates very beautiful 2D layouts of networks:

Image:LGL_protein_homology_color_thumbnail.jpeg Image:LGL_scop_sunid_heirarchy_thumbnail.jpeg Image:LGL_full_size_thumbnail.jpeg Image:LGL_zoom1_thumbnail.jpeg Image:LGL_zoom2_thumbnail.jpeg Image:LGL_zoom3_thumbnail.jpeg

  • Dynamic MS + MS/MS viewer: Create a dynamic visualization tool (in 2D or 3D) that allows a user to get more information about each of the MS/MS hits in a file. For instance, pep3D gives a birds eye view of the peptide hits, but we'd like to be able to interrogate each of the hits (i.e., bring up a mascot like view of the hit). [John P. - I have looked into this and have some thoughts]
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