[open-science] Open repositories

Fri Jul 9 10:12:16 UTC 2010

i'd strongly encourage checking out these 2 links for more on paper-vs-code-vs-data in open science, including license issues:

http://www.ijclp.net/issue_13.html ("licensing for scientific innovation")

http://www.stanford.edu/~vcs/Conferences/RoundtableNov212009/ (documents associated with a one-day "roundtable" meeting on open paper-vs-code-vs-data @ yale law school)

best

C

ps: some examples of "compendia" (examples of making an open archive of the paper, code, and data) include:
1. http://thedata.org/home
2. http://rr.epfl.ch/

________________________________________
Chris Wiggins
Associate Professor

Department of Applied Physics
and Applied Mathematics;
Center for Computational Biology
and Bioinformatics
Columbia University
http://www.columbia.edu/~chw2

chris.wiggins at columbia.edu
tel: 347.878.1256
________________________________________

On Jul 6, 2010, at 6:57 PM, Peter Murray-Rust wrote:

> 
> 
> On Tue, Jul 6, 2010 at 11:15 PM, Jessy Cowan-Sharp <jessy.cowansharp at gmail.com> wrote:
> didn't want to hijack the other thread so i changed the subject line, but i'm curious (and perhaps this is a naive question): 
> 
> You didn't actually change the subject so I have done so 
>  
> what open access repositories are there which people recommend, besides, say, arxiv.org? arxiv.org itself doesn't seem to have a strong (or at least not explicit) stance on licenses and such. and are there any OA archives where people can submit their code/data along with their paper (in such a way that it is formally associated with that paper?)
> 
> 
> It's probably useful to differentiate between code/data/documents. The current usage is:
> 
> open access - papers
> open source - code
> open data     - data
> 
> OpenSource is usually stored in specialist software repositories, which should have  a powerful versioning system (SVN or better Mercurial or Git). Typical repos are Sourceforge and bitbucket. These repos *could* be used for otehr material (such as data or documentation but this is probably not a good idea technically, as there is no good text search facility, etc)
> 
> OpenAccess material is usually stored in paper-oriented repos (DSPace, Eprints, Fedora) and are commonly found in Universities and similar insts and run by LIS staff. They are totally unsuited to software and data (go on, someone, ask me why!)
> 
> OpenData is relatively new. The problems of storing it are considerable and largely unsolved. Problems include versioning, dynamic updating, metadata, formats, lack of specialist knowledge (there are (tens of) thousands of common formats (e.g. several hundred alone in chemistry). This is my speciality and I don't know the answer. I suspect it will be domain-specific (e.g. biosequences, etc, are well supported at present, chemistry has possiblle solutions but there are rabid anticommons interests in chemistry, particle physics is huge, climate is hyperpolitical, etc.) OKF is as good a place to start as any (though we can't store huge datasets and are more likely to address metadata).
> 
> 
> 
> 
> -- 
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
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> open-science at lists.okfn.org
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