Archive for June, 2006

My Lab work has finnished!


Hurray! At last I have ran my final 2D gel for my PhD, no more crying over spilt acrylamide. Only joking I have never spilt acrylamide :). Now I have three months left to do nothing but bioinformatics and of course the dreaded write up. Maybe a could design an ontology that could infer my thesis from all the data I give it. Any way I though I would post a picture of my last gel so you can all marvel at a bioinformatician who can run 2D gels.


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Flock — The web browser for you and your friends

I have downloaded the Beta 1 (v0.7) of the web browser Flock, to have a look and play with it. This very post has been used within Flock by simply right clicking over the web page and choosing the option “blog this”. So as I type this I am looking forward as to how it will appear. The news feed options are definately nicer than how firefox handles them. I currently use bloglines for subscribing to feeds so I will test out how. I have also used Google browser sync and I am really liking it, so I have to find a similar one for flock. Oh well back to playing with my new toy. I will let you know my future opinions

Blogged with Flock

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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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Ontology of Scientific Experiments

NewScientist of all places are talking about ontologies. Specifically An ontology for scientific experiments.

"Called EXPO, it can be used to translate scientific experiments into a format that can be interpreted by a computer."

Wow! translate experiments, that's impressive I would love to find out how the scrawny hand-writing, contained inside the standard lab notebook, dog-eared and drenched in all manner or reagents, gets translated into an ontology, that's more impressive than the ontology itself.

However on a more serious note, I agree with the concept, that something like this should exist. It would definately help in dissemination and analysis of data (providing the data is freely provided and in a standard structure of format), but this kind of process, an ontology for all of science, would have to have a major open development across all scientific disciplines, as FUGO (Functional Genomics Investigation Ontology) are doing, in order to be agreed upon and for the claim that it represents all scientific experiments.

Going by the article, and snooping around the EXPO site, a cross discipline development process doesn't appear to have taken place, or planned for the future (my apologies if this is not the case). And according to the article it has been tested on two use-cases, one on particle physics and one on evolutionary biology, this must be the only wet-lab science that exists these days. It would be interesting to see if the large scale collaboration effort of FUGO agrees with or already has a similar structure to EXPO
A quote at the bottom of the article says "Software to speed up this process could be a big boost ", I think he meant to say, "This would be impossible without software being available from the wet-lab bench, to data storage, to the publication process".

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Big Up

Hey this is just note that fellow bioinformatician and apparently bon vivant (at first glance bon voyeur), geek and chappist, Dan Swan has spotted my blog, so he goes on the blog roll.

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Journals but not as we know it

There is an interview on Wired magazine on Harold Varmus, the Nobel laureate and former director of the National Institute of Health. The premise of the article is not on his prize winning exploits but rather his involvement and the setting up of PLoS (The Public Library of Science), which is an open access scientific publishing platform. Many comments and opinions exist on PLoS and its impact but I think the most interesting section of the article is on the new PLoS journal which is due to be launched in the summer called PLoS ONE.

"And this summer, Varmus and his colleagues will launch PLoS One, a paperless journal that will publish online any paper that evaluators deem “scientifically legitimate.” Each article will generate a thread for comment and review. Great papers will be recognized by the discussion they generate, and bad ones will fade away. "Our mission is to transform how science publishing is done,” Varmus says. “We aren’t trying to torpedo the industry. But we are definitely going to change it.” "

This effectively destroys the current peer review system and allows for continuous peer review or an article as more knowledge and opinions develop over the years. It will also permit comment by "experts" that would not have been involved in the traditional peer-review process.

Although there also could be a dark side to the comments where "my paper is better than your paper", or biased comments where a competing interest is evident.

All in all however, I think this is a massive step forward and a massive shake up of the scientific publication process. I hope there is a strong emphasis on providing all the available data in the appropriate standard formats for the domain and if this is the case then I am all for it.

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