Archive for category Thesis

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.


Standard Open(ed-up) Science

OK, so it is not quite up to the minute as-you-do-it-you-publish-it open science. However, I plan to make my data that I generated during my PhD (just finished) open and available, and in writing this post I am making some what of a public commitment to do so. Once difference though, from some of the open science efforts that I have seen so far, is that I will be publishing my data, conforming to the Proteomics Standards Initiative(PSI) MIAPE guidelines for gel electrophoresis (MIAPE GE.pdf) recommended reporting requirements. The data itself will be represented in XML using the PSI recommended gel electrophoresis Mark up Language (GelML), and using terminology from sepCV and OBI should mean the data set is computationally amenable. I was involved in the development of these specifications so I suppose I should be leading by example and be the first one to publish a complete gel electrophoresis proteomics dataset.

When finnished, I would have liked it to be published some where like Nature Preceedings, however they only accept proprietary Microsoft files and pdfs rather than XML documents. I also though of creating a Google code project for it, but it seems quite elaborate for something nobody else would be contributing to and once completed would be rather static. Any suggestions are very welcome.


Connotea: social bookmarking system for scientific literature

I have recently started using Connotea which is what they now describe as ” Free online reference management for clinicians and scientists”. I remember seeing a presentation on Connotea at the Data webs workshop I attended, (excellent day of talks and discussions), where Connotea was described as a “social bookmarking for scientists”. I wasn’t overly convinced to use it then and my initial perception was that it was for scientists, so why not use  On a more recent, closer look, I see they have re-branded (or re-advertised) and are concentrating on tagging publications and providing exports to various reference managers, particularly bibtex, my favourite. This feature has convinced me to give it a try and as I am writting my thesis at the moment and I am really putting it through its paces.

I am liking it so far and definately “Discovering” new resources based on my tags. Hopefully I will never need to ask the questions again “Where did I put that paper?” or “I knew I read a paper about ontologies but which one was it?”


The final count down

I have created a breakdown of my final few months of my PhD in the form of a gantt chart. I found this exercise pretty useful to outline all the loose ends I have and the bits of work I still have to do. If I stick to this timetable, which is probably easier said than done then all the work should be finished by August which would give me all of September to write up, or rather to start the write up process. When I produce the chart I though it might be useful to do one based on how long it takes each of my supervisors to review each chapter, I may put this on my blog, and maybe the public documentation of the review process, may start a competition which result in the chapters getting reviewed faster.

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