Archive for category Thesis
Open-ed gel electrophoresis data
Posted by peanutbutter in bioinformatics, data standards, FuGE, Google, notebook, online, ontology, open data, open science, Proteomics, subversion, Thesis on April 30, 2008
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
Posted by peanutbutter in bioinformatics, data standards, open data, open science, Proteomics, Thesis on January 28, 2008
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.
The final count down
Posted by peanutbutter in Thesis on May 30, 2006
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.