Open-ed gel electrophoresis data

Several months ago – about 3, I made a public commitment to make the data I have generated during my Phd open and available online. Well I have not ignored this and in the interim I have been investigating various ways I can do this. Not only do I want to make it available but I want to structure it in a standard form, namely the gelML format. In addition, I was involved in developing it the specification and therefore, I have somewhat an obligation to use it. As it is an XML transfer format I needed to be make changes and revision it, like developing code, so in that sense recording the data on a wiki or blog would not be appropriate. For this reason I have chosen to create a google code project for gel electrophoresis data and do everything in subversion. You can browse the subversion repository or check it out anonymously. The geML file that will eventually (as its still very much a work in progress) contain the data is here. As I am doing this, I though I might as well publish my lab book while I was at it. This will be done using LateX and the pdf that gets generated can be found here.

To date, this is still a work in progress and a reverse engineering project, as the experiments are not being done live. It may take a while to complete but in the end I hope presenting my data in gelML and making my labbook available can be more of a benefit than decomposing for years on cellulose.

  1. #1 by Jean-Claude Bradley on May 1, 2008 - 6:00 pm

    Why do you say that a wiki is not appropriate for keeping track of versions?

  2. #2 by peanutbutter on May 2, 2008 - 8:43 am

    @Jean-Claude Bradley. I realise this might not have been clear, when I mentioned “data”, I actually mean an XML file, as opposed to the information in the lab-book. I need to be able to edit the XML using an XML editor, check for consistency and validate the XML document against the GelML XML-Schema, and revision my changes that way. It is these issues rather than versioning which led me to chose a code revisioning set up. What I am trying to do is actually make the data in XML available, so that I why I chose the google-code project. After I had set it up, I thought I might as well expose my lab-book as well. I could have done this using a wiki, however, I thought it would be easier to continue to use the same set up, rather than any endorsement against using wikis. Sorry for the confusion.

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