Archive for category Google

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.

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RSS readers

I have outlined my growing tendency at the minute to handing over applications to the “Internet cloud” in an earlier post.

I prefer using web-based applications because I tend to jump from several machines throughout the day at work and then use a different machine at home. Having applications, floating in the ether cloud, means moving around is considerably easier. I have been using bloglines for quite a while now for my RSS feeds. I did have a early look at Google reader when it first launched, but I felt then it was not quite what I wanted and definitely not as good as bloglines at the time. However a re-visiting of Google reader over the last week or so has dramatically changed my perception. Re-vamped with a new interface (similar to bloglines) has made reading posts alot easier. All the post from your subscribed feeds are actually saved, by default and don’t disappear once read, unlike in bloglines (unless you check the “keep new” box). I think the biggest feature for me is the ability to tag posts, combined with the saved posts facility, this should prove to be a very handy source of reference rather that just an “recent-post viewer”.

A new feature that has just been added to Google reader is the offline mode. Working in conjunction with Google Gears this provides the ability to read the last 2000 recent items, a feature I am looking forward to testing during the flight to ISMB in a few weeks.

If you use another RSS reader or have an opinion on Google reader then let me know.

With using gmail, and calendar, with trying out Google reader (and probably switching from bloglines), using google docs and spreadsheets more everyday, there is every danger that my cloud is going to be raining google. With the added prospect of Google presentations round the corner will it be long before I am floating off to the Google OS cloud?

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CARMEN

Today is my first day in my new job as a RA for the CARMEN project, which stands for Code, analysis, repository and modelling for e-Neuroscience. My role in this exciting project, is as a Metadata researcher for experiment context, which should involve ontology development and data representation in neuroscience.

Just as a matter of interest I thought I would compare bioinformatics and neuroinformatics on Google Trends. Looks as if I have plenty of work to do!

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Synchronized

Google has just released the Google Browser Sync extension for Firefox. Google Browser Sync for Firefox is an extension that continuously synchronizes your browser settings – including bookmarks, history, persistent cookies, and saved passwords – across your computers. It also allows you to restore open tabs and windows across different machines and browser sessions.
This extension allows you to save your bookmarks, history and passwords on Google servers, effectively giving you a 'roaming profile,' which you can sync on any computer running Firefox (and the extension, of course)."I think this could be a very useful idea as, I flip between a dual booted Windows/Ubuntu desktop, the same for a laptop and in the wet-lab an E-Mac, and it would save me having to keep my bookmarks on a USB flash drive, although I am not sure about the bit on saving passwords. I will give it a go, let me know if you find it useful too.

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