Archive for the “Links” Category

It’s no secret that my desire to blog was interrupted by the arrival of FriendFeed and Twitter in my daily routine.  The former allows me to aggregate not only content from those people I really like to follow online, but also allows me to push most of my RSS-isable online content to the same place.  I should probably just push most of it here (the flickr tab is a new introduction, as is the Twitter feed sidebar on this blog) but I haven’t found a sufficiently pleasant life-streaming theme for WordPress yet.  Twitter on the other hand really does allow me to push my ramblings, day to day thoughts, and status updates to the world in a way that is much more immediate (and in some ways pleasing) than blogging.  I don’t mind if you don’t get it, Twitter is fun, and a damn site more useful than MSN messenger.

The only thing about FriendFeed is that whilst it aggregates a lot of personalised content from my cohort of tech-savvy friends, it hasn’t quite turned into an RSS aggregator par excellence.  A vast swathe of my online time is still spent consuming RSS feeds in Google Reader.  So as an incentive to start blogging again (with a low barrier of entry ;)) I thought I would share a few of my favourite feeds that keep me coming back again and again, some of which hopefully are novel and useful.

I organise my reads by broad themes, and the first one in Google Reader happens to be ‘Arts’.  This covers, for me,  contemporary art to music (which I won’t *cough*Torrentech*cough* go into) to literature (and by literature I mean Sci-Fi ;)) and some stuff in between.

First up is the BALTIC forthcoming events feed.  The BALTIC is a fantastic contemporary art gallery on the banks of the Tyne, which splits Gateshead (my stomping grounds) from Newcastle (where I actually work).  Housed in an old flour mill on the Gateshead side, the BALTIC is one of my favourite places in the North East and every time I go I feel privileged to have such a great gallery so close to home.  The feed itself serves up good notice of forthcoming exhibitions, but for the real skinny on lectures, workshops etc. then the Facebook group or mailing list tends to have more details than just the exhibitions.  It would have been nice if they hadn’t switched their RSS feed URL with zero warning in August though.  A last post detailing the new  URL would have been a nice touch.  Or maybe a PURL for the feed perhaps?  It took me a little while to notice as new installations don’t come around that often!

Charlie’s Diary is the excellent blog of Charles Stross – one of my favourite British SciFi authors.  Aside from the fact that he writes great fiction, this is a man who writes his own blog engine, loves vi, predates Linux and once was gainfully employed crafting crufty Perl scripts to provide one of  the earliest online payment systems on the internet.  This man is not only an author, but a geeks geek, and politically astute enough to understand the ramifications of advancing technologies.  This blog is worth a read, regardless of whether you are a fan or not.

The final two links in this category deal with my current mild obsession which is digital photography.  Having recently splashed out on a very low end digital SLR (a Nikon D40 if you care) the chance to marry obscene technological geekery with something vaguely artistic has been a powerful draw for me.  It’s lead to a number of magazine and book purchases, but there’s nothing like the internet for free and useful information.

So the Digital Photography School feed is first up.  For me this is just the best site for a continual stream of information for my new hobby.  Split into 3 main sections the site slices and dices it’s articles into “Photography Tips and Tutorials”, “Cameras and Equipment” and “Post Production”, I really only look at the first of these.  I won’t be making any more equipment purchases other than a tripod, remote shutter release, neutral gradient density filter, polarising filter, telephoto and macro lenses (and the depressingly expensive  50mm AF-S f1.4G Nikkor that I crave) for a while.  OK so it’s basically so that I don’t add any more expensive items to my Amazon wish list, and the fact that I can pretty much work out how to use Lightroom by myself for now.  I am completely awash in a world of f-stops, ISOs, apertures and shutter speeds, and it’s this site that is helping me through it currently.

The second is a proper photography blog – the feed of the Newcastle Upon Tyne Daily Photo site.  This is a photoblog of local (well to me!) sights, with two main contributors.  Now when these girls say ‘Daily’ they mean ‘Daily’ I don’t think in the months that I’ve subscribed they have ever missed an opportunity to post a view of Newcastle and its surrounds.  Yes, there’s been an occasional repost, but not one that I’ve seen twice yet!  Everything is covered from the Quayside, the city centre, pubs, bridges, the lot.  Sometimes there’s views of the city and places that I’ve just not noticed, other times I’ve had to grab the camer and go out and grab similar shots.  The photos might not always have stunning composition, but it’s just nice to be reminded that Newcastle is a beautiful northern city, proud of it’s heritage and definitely my favourite city in England.  A few of my own photos taken over the last few months have ended up in this gallery on flickr but I need to take some more.  I’ve also got some photos of Gateshead here and the Great North Museum (Hancock edition) here.  Next time they invite reader submissions, I’m going to see if I can get one of my shots in…

So yes.. my ‘Arts’ section, not so large you see!  Wait until I get onto the feeds in the ‘Geek’ section eh?

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This came via the “R Project for Statistical Computing” group on LinkedIn, but it definitely seems there is a hashtag for all occasions these days on Twitter.  Today it’s largely been connected with the election fallout in Iran on Twitter, with massive trending topics and a significant segment on the Channel 4 news devoted to it.

Getting back to things of a more academic bent, for those of us interested in R, posting those 140 character frustrations, hints, tips and questions – these can be aggregated with the #rstats hashtag allowing you to search Twitter traffic for statistical topics of interest with ease.

I seem to be spending a lot more time with my head in R these days, my “BioConductor Case Studies” book has just arrived, and the chunk of the day that wasn’t spent cursing a fritzed ext3 partition on an LVM volume, or installing our new monster machine was spent in R, answering questions from my Maths and Stats summer student.

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I’m terrible for keeping up with my podcasts, and only just got around to part one of the four part “In Our Time” Darwin podcasts from Radio 4 yesterday.  Consequently when I went around to get parts two, three and four – iTunes had no knowledge of them any more. I tried to find links from the IOT RSS feeds – but all the links to the audio had been removed.

This morning, poking around on the ‘Listen Again’ part of the site, I found the embedded Flash players that would allow me to listen to the podcasts in my browser.

I wanted them to listen to on the way to work however!

A bit of digging around through the HTML and subsequent XML playlists, I managed to find downloadable, transferable mp3 content.  Linked here for your listening pleasure:

Programme 1

Melvyn tells the story of Darwin’s early life in Shropshire and discusses the significance of the three years he spent at Cambridge, where his interests shifted from religion to natural science.

Programme 2

Darwin’s expedition aboard the Beagle in December 1831 and how his work during the voyage influenced and provided evidence for his theories.

Programme 3

How Darwin was eventually persuaded to publish On the Origin of Species in November 1859 and the book’s impact on fellow scientists and the general public.

Programme 4

Melvyn visits Darwin’s home at Down House in Kent. Despite ill health and the demands of his family, Darwin continued researching and publishing until his death in April 1882.

Happy timeshifting Darwin Day!

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And that’s a rare enough concept, but this made me laugh

The suggestion in the discussion was that the best people to run a University email service was the CS dept:

Don’t. The CS department is interested in education and research. They may come up with an innovative solution and write a few papers about it – then abandon it, leaving it with poor documentation, a bad interface, hundreds of bugs, and idiosyncratic and non-standard elements.

IT is not CS. IT is a service.CS is a discipline. Asking the CS department to run the academic IT systems is like asking the English department to run the library. It’s a non-starter.

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With grammar test applications currently exploding all over Facebook, their only purpose to be harvesting all your juicy personal data whilst you prove to your friends that aged 34 you really can tell the difference between “their, there and they’re”, it’s nice to come across a simple blog that holds up some of the greatest abuses of quotation marks ever seen (and doesn’t need to be sent to 10 of your friends in order to view it).

Enjoy them at The “Blog” of “Unnecessary” Quotations.

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xkcd. How does it keep READING MY MIND!

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Finally, a useful application on Facebook! Simply add this application, check the papers that it spits back as being yours, press ‘ok’ and voila – your Facebook page now looks like a gaudy CV!  You can also add papers by PMID if it doesn’t pick up your entire publication output.

Originally spotted on ‘What You’re Doing is Rather Desperate‘ a blog title that I have always loved being a bioinformatician who has to deal with biologists!

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This is an accurate representation of what I have been doing since I have been away.  From the always awesome site xkcd of course.

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So according to the BBC today, the Archbishop of Wales trots out the usual Christmas bollocks about how the atheists are ruining Christmas for the masses.

Choice quotage:

The archbishop said “atheistic fundamentalism” was a new phenomenon.

He said it advocated that religion in general and Christianity in particular have no substance, and that some view the faith as “superstitious nonsense”.

As well as leading to Christmas being called “Winterval,” the archbishop said “virulent, almost irrational” attacks on Christianity led to hospitals removing all Christian symbols from their chapels, and schools refusing to allow children to send Christmas cards with a Christian message.”

What is particularly annoying about this is that Church leaders whining about Christmas being ruined is not a new phenomenon at all, it happens every year without fail, for as long as I can remember. It’s also patent rubbish. This business about Winterval, the banning of nativity plays etc. etc. etc. just isn’t true. The last time I checked 25% of primary schools were still Anglican, presumably therefore allowed to peddle whatever message of Christmas they like to their indoctrinated ‘consumers’.

The whole ‘Winterval’ thing is laughable – in 1997 Birmingham City Council decided to use this term to incorporate all the multi-faith (and secular!) celebrations over the winter period with an umbrella term. It was never in any way meant to denigrate, sideline or replace Christmas (or Eid, or Diwali or Guy Fawkes Night). Only the Daily Mail brigade took it that way, and 10 years later senior Church members are still lying about it.

Chapels in hospital are removing Christian symbology? Well I’m aware that some hospitals have multi-faith ‘prayer areas’ where presumably Christians, Muslims and atheists who want a bit of peace and quiet can go and think/pray/whatever, but surely Christian trappings would be inappropriate in this context? I’ve worked in plenty of hospitals with chapels and mosques, so where, pray tell, is the Bishop getting these crazy ideas from?

Atheistic fundamentalism is only getting fundamentalist because we’re now angry with the propagation of the same old lies, half truths and cries of ‘political correctness gone mad’ that we’re no longer prepared to humor them. These people must be held up, pilloried and harrassed with facts and logic until the stupid, banal and untrue statements are finally laid to rest.

I love Christmas, I do, I really do, but I no longer associate it with any Christian message. That’s for me to decide to do and practice. If you want to go to Church, think about the baby Jesus that’s all fine, but don’t lie about how atheistic observation of Christmas is ‘ruining it for the rest of you’.

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I notice that PLoS Computational Biology is publishing a series of ‘Getting Started in‘ articles for bioinformatics/computational biology.

“The aim of each article in the “Getting Started in…” series is to introduce the essentials: define the area and what it is about, highlight the debates and issues of relevance, and provide directions to the most relevant books, articles, or Web sites to find out more. The series will not include review articles or detailed tutorials; these are available in the Education section of the Journal. Rather, each “Getting Started in…” article will aim to be a cache of “go to” information for someone for whom the field is completely new.”

The first one is a neat little excursion into tiling array analysis for platforms such as Nimblegen et al., it is relatively brief, but supported by excellent references which people new to the field will find extremely useful.

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