Brief Hardy Heron notes

Nothing exciting - just a couple of notes on the Ubuntu upgrade experience from 7.10 to 8.04.

Now officially living in my browser

Firefox screenshot, from left to right: Vertical tabs, courtesy of Vertigo - because you can never have too many tabs Main window: the feeds roll into GReader On the right, almost all the functionality of FriendFeed (except search) in fantastic new extension MySocial 24×7 On the right? Yes, because sidebars look better on the right IMHO, made possible by MultiSidebar

Tenuous bioinformatics connection: well, you work more effectively if you’re happy with your browser setup

App Engine for research #2

ResolveRef, a RESTful way to resolve PubMed queries by journal, year, volume and page is Andrew’s port of OpenRef to App Engine. Simple, but very effective and a nice illustration of how to get to grips with the App Engine environment.

Keep those “App Engine apps for researchers” rolling in, folks.

An R Wiki

It’s been ages since I visited the R website, so I don’t know how long they’ve had a wiki. It’s built using DokuWiki, one of my personal favourites.

This is a great leap forward for R documentation, which is somewhat notorious for being (a) difficult to find and (b) difficult to understand when you find it. If you’re a power R user and have a spare moment, please contribute.

Around the open science, social web

This blog seems to become more about social networks/open science and less about bioinformatics every week. Perhaps that’s no bad thing. Here’s a few highlights from the activity stream this week.

• From Depth-First: User-Created Compound Monographs on Chempedia.net on the Web 2.0 approach to chemical encyclopedias
• Post of the week: in response to One Big Lab, Cameron on the science exchange
• In response: Deepak on micro-funding; thankfully one of us has a business mind
• Science Commons asks are you part of open science?
• And the iPlant Collaborative takes affirmative action on science collaboration (some nice-looking jobs at CSHL posted there)
• Nature Network announce plans for a European Science Blogging Conference
• Also from Nature Network, a record 100 comments for Jennifer’s post; admittedly the last few are silly ones to get her over the line
• UsefulChem points us to an article in Cell on open-source drug discovery
• From Bioinformatics, a follow-up to the “404″ study (thanks Paulo!); take-home message is that academics probably shouldn’t run webservers
• Rosie’s long, blog-less teaching stint is over; she returns with a discussion about making shared code readable
• Finally from the “things that made me laugh” department: Facebook group pop songs as graphs (thanks Graham)

Two great open science resources

The Twitter + FriendFeed combination is proving to be a very useful information stream; not just from other people but as a reminder of what I thought was worth sharing. Two links from there that I think deserve wider attention:

• One Big Lab proposes that we become, well, one big lab - and has some ideas as to how that might work.
• From the OWW wiki, an excellent article on python in computational biology. This has been presented at Pycon 2008 and is also a companion article to a paper in PLoS Computational Biology. Imagine if everyone described their methods in this detail.

Deepak has some commentary on what we’re now calling the “bio-twitterverse”.

First past the post…

…with a biologically-relevant application for Google App Engine, is Euan with pycite, a port of Connotea. Man, this makes me want to learn Python fast.

More thoughts and commentary at Deepak’s blog.

What does it all mean?

My Tweet Cloud is probably trying to tell me something important. But what? Thanks to Attila for pointing to the resource.

Aggregating the aggregators

Cameron has a good discussion of lifestream aggregators in a research context.

I have a non-research problem: two apps (FriendFeed and Profilactic), doing essentially the same job, each with features that make both worthwhile. I like Profilactic for these reasons:

• Design and appearance (YMMV)
• Ability to fetch content from my friends if they use the same services that I do, without having to get them to subscribe to Profilactic (killer feature IMHO - FriendFeed has the “imaginary friend” to do a similar job, but way less convenient)
• Huge number of services that can be aggregated
• Ability to aggregate any feed without giving it a misleading label (FriendFeed will aggregate any feed too, but insists on titling items as “blog post”)

On the other hand, FriendFeed has these great features:

• Search
• Comments, leading to meta-conversations; I was initially sceptical of this but I’ve found a lot of value in it

So my latest experiment: use my Profilactic mashup (available as a feed) as my only item in FriendFeed. That way my stuff gets aggregated the way I like it (Profilactic) and each item is available for search and discussion in FriendFeed. The only downside is that every FriendFeed item is labelled as “a blog post on Profilactic mashup”.

This may be madness, I may be spending way too much time on this, but let’s see how it works out.

update 14/4/08: not bad, but FriendFeed works best when aggregating individual feeds (e.g. Flickr photos are displayed); so it’s back to that!

Bio::Blogs #20

Bio::Blogs #20 is up, over at Pedro’s place. Lots of interesting material from the bioinformatics blogosphere this month, so go and have a read.

As I suspected, now that Pedro is a bright young US postdoc (no doubt working 18 hour days), his time commitments have pushed Bio::Blogs down the priority list. If anyone can help out, or suggest alternatives to the current system of monthly compilation by one person, do get in touch with him at his blog. I wonder if we can use some of the aggregated content at places like FriendFeed or the Nodalpoint news aggregator as an easier way to generate monthly summaries of activity?