Prince:Open Computing Projects: Difference between revisions
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{{PrinceLab}} | |||
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== | ==General== | ||
* Develop a wiki that uses markdown for the front-end and git (preferably abstracted) for the backend. | * '''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. | ** Should be extremely easy to use, organize, clone, share, etc. | ||
** File structure should be easily navigable within the repository and on the web interface. | ** File structure should be easily navigable within the repository and on the web interface. | ||
** Seems like a candidate: [http://github.com/georgi/git_store git_store] | |||
* Any of the projects on [http://wiki.github.com/rdp/ruby_bounties/ruby-bounties Ruby Bounties] | |||
==Numeric Computing== | ==Numeric Computing== | ||
* Figure out how to manipulate [http://narray.rubyforge.org/ NArray] objects from within Inline. | * <s>'''NArray in Inline''': Figure out how to manipulate [http://narray.rubyforge.org/ NArray] objects from within [http://www.zenspider.com/ZSS/Products/RubyInline/ Inline]</s> | ||
* Create a tutorial for [http://narray.rubyforge.org/ NArray] based on [http://narray.rubyforge.org/SPEC.en the methods page] | * Implement NArray completely within [http://github.com/ffi/ffi FFI] (and/or [http://github.com/remogatto/ffi-inliner FFI-Inliner]). | ||
* Create a [http://numpy.scipy.org/ NumPy] equivalency document showing how to do things in [http://narray.rubyforge.org/ NArray] and NumPy. | * '''NArray Tutorial''': Create a tutorial for [http://narray.rubyforge.org/ NArray] based on [http://narray.rubyforge.org/SPEC.en the methods page] | ||
* '''NArray <=> NumPy Equivalency''': Create a [http://numpy.scipy.org/ NumPy] equivalency document showing how to do things in [http://narray.rubyforge.org/ NArray] and NumPy. | |||
** This could be based on the NumPy [http://docs.scipy.org/doc/numpy/user/ User Guide] and/or [http://docs.scipy.org/doc/numpy/reference/index.html#reference Reference] | ** This could be based on the NumPy [http://docs.scipy.org/doc/numpy/user/ User Guide] and/or [http://docs.scipy.org/doc/numpy/reference/index.html#reference Reference] | ||
** Extend NArray as necessary so that all useful functionality of NumPy is duplicated in NArray or separate gems. | ** Extend NArray as necessary so that all useful functionality of NumPy is duplicated in NArray or separate gems. | ||
==Visualization== | ==Visualization== | ||
* Get [http://lgl.sourceforge.net/ LGL] ([http://sourceforge.net/projects/lgl/ sourceforge page]) working again standalone, or get it working as a plugin for [http://www.cytoscape.org/index.php cytoscape]. LGL creates very beautiful 2D layouts of networks: | * '''Resurrect LGL''': Get [http://lgl.sourceforge.net/ LGL] ([http://sourceforge.net/projects/lgl/ sourceforge page]) working again standalone, or better yet, get it working as a plugin for [http://www.cytoscape.org/index.php cytoscape]. | ||
<b>**NOTE**</b>One alternative may be the <b>sfdp</b> algorithm implemented in [http://www.graphviz.org/ graphviz]. ([http://www2.research.att.com/~yifanhu/PUB/graph_draw_small.pdf pdf describing the technique]). | |||
LGL creates very beautiful 2D layouts of networks: | |||
[[Image:LGL_protein_homology_color_thumbnail.jpeg]] | [[Image:LGL_protein_homology_color_thumbnail.jpeg]] | ||
[[Image:LGL_scop_sunid_heirarchy_thumbnail.jpeg]] | [[Image:LGL_scop_sunid_heirarchy_thumbnail.jpeg]] | ||
| Line 19: | Line 30: | ||
[[Image:LGL_zoom2_thumbnail.jpeg]] | [[Image:LGL_zoom2_thumbnail.jpeg]] | ||
[[Image:LGL_zoom3_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, [http://tools.proteomecenter.org/wiki/index.php?title=Software:Pep3D 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] | |||
Latest revision as of 08:28, 14 July 2010
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
- Resurrect LGL: Get LGL (sourceforge page) working again standalone, or better yet, get it working as a plugin for cytoscape.
**NOTE**One alternative may be the sfdp algorithm implemented in graphviz. (pdf describing the technique).
LGL creates very beautiful 2D layouts of networks:
- 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]
