Archive for February, 2008

Zotero library re-visioned

Posted by peanutbutter in backup, bioinformatics, howto, Journals Publishing, library, reference, Social Bookmarking, Social Media, subversion, zotero on February 22, 2008

I have been wanting to use Zotero now for a while for my reference library but could never work out how back up my library using subversion. My life is contained within subversion, I do not know how I could have possibly survived before all my work; code, presentations, papers, images and not to mention my thesis, is all perfectly backed up and re-visioned and floating happily in the cloud available to me from any machine. Zotero installs itself inside the firefox profile which makes it difficult to revision within the C:\\my-subversion” folder. What I decided to do was to create a new firefox profile (instructions here) within my-subversion folder then install zotero creating:

C:\\my-subversion\firefoxprofile\zotero

I then only added the zotero folder to my subversion repository. You could always revision your firefox profile but I decided not to. Now every time I add a new item to zotero the my-subversion folder indicates there has been a change and requires a commit. Obviously every time you add a pdf file to the library you will actually have to “SVN add” the file itself. This is not a problem for me as I try to keep my library light and not store to many pdfs.

I am also going to try and use zotero as an interface to my subversion repository, describing and tagging documents and code that I write, but more specifically presentations, so no more trying to work out what is contained in “Presentation1.ppt” or what file name I gave to that talk on data standards which I have to give tomorrow!

I am tagging my hard drive via Zotero, its just one big cloud.

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sshh!, dont tell anyone about Data Sharing for Computational Neuroscience

Posted by peanutbutter in bioinformatics, CARMEN, data standards, neuroinformatics, ontology, open data, open science on February 18, 2008

I described in an earlier post that data sharing in Neuroscience is relatively non-existent. Some commentary on the subject has appeared since then via the 2007 SfN Satellite Symposium on Data Sharing entitled Value Added by Data SharingLong-TermPotentiation of Neuroscience Research, published in Neuroinformatics. I was also excited to see an article published last week Data Sharing for Computational Neuroscienc, also in Neuroinformatics. However, there is a caveat or two. Apart from ignoring all the data representation issues presented in other domains such as bioinformatics, the re-use of data models such as FuGE, or contribution to ontology efforts such as OBI, all these articles are not open access! How ironic, or should that be how embarrassing. Phil also covers this issue in his blog.

Oh well, looks as if there is still a challenge in the domain of Neuroscience for access to valuable insights into information flow in the brain. Who want to know how the brain works anyway? You can always pay $32 to springer if you want to find out.

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