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I spend most of my Wednesdays looking for errors, from the blatant to the egregious, in recently-deposited protein structures in the PDB. Sometimes, I feel the urge to get in touch with the people who deposited the structure; the PDB lists this in the form

AUTHOR Y.T.MEHARENNA,T.L.POULOS

and it takes quite a lot of googling to track these authors down to their current institution and deduce, for example, their email address. In this case I've found them - Meharenna is not so common a name as to have multiple false-positives in Google Scholar, and has only changed institutions a few times.

I guess that some text-miner must have done a mining of affiliations, so you could click on 'YT Meharenna' and find 'Yergalem T Maharenna published nine papers between 1998 and 2007 (list); common collaborators include Thomas Poulos (2004-2007) and Gianfranco Gilardi (2001). Was affiliated with UC Irvine on papers published in 2004-2007 and Imperial College on papers published in 2001'.

What's the name of the site that presents the results of this mining?
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Anyone want a brand-new copy of K J Parker's Colours in the Steel ? An unobserved shopping error at Amazon meant that I ordered two copies. Yours for a pint.

His trilogy beginning with Devices and Desires caught me by page three of the first volume when I picked that up at a con a few years back, and was good enough to the end that I bought this earlier trilogy of his sight-unseen.

(I had to check his gender; for some reason initials make me assume a writer is female, and the writing style, possibly by comparison with [livejournal.com profile] papersky, struck me as ineffably feminine)
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I know I have a number of Scandinavian readers and a number of readers with reasonable experience in eastern Europe, so I'll ask here.

There are two things I'd like to do this year: a few hundred miles of cycle touring somewhere around Denmark-ish, and some standard city-hopping-by-train backpacking in Ukraine: Lviv, Kiev, either Yalta or Odessa, Kamyanets-Podilsky if I can figure out how to get there.

I was thinking Denmark at Easter and Ukraine in the summer, but the more I look the more it seems sensible to do them the other way round; Ukraine in August is clearly very hot and the south coast covered from Odessa to Mariupol with every Russian in Russia taking their summer holiday, whilst Denmark in April seems perhaps on the blusterous side, and plotting crazy cycling in August gives me four months of English spring weekends in which to improve my cycling stamina. Am I missing something critical?

Is there anyone reading this with knowledge of the area who can suggest whether it would be more fun to cycle from Copenhagen down to Lubeck, Kiel, Flensburg, Odense, back to Copenhagen, or to go across to Malmo and up the east coast of Sweden to Stockholm, which looks as if it could be done as ten fifty-mile days (though I need better-than-Google maps to see how near to the coast you can go and how you can avoid the E22), then jump on a train back?

Are there likely to be problems with taking a hired bike across the Denmark-Sweden or Denmark-Germany border?
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I made Sunday lunch for [livejournal.com profile] mobbsy, [livejournal.com profile] sonicdrift and my housemate-brother Ben; 1.3kg of lovely leg of lamb from the local butcher, rubbed with garlic and thyme and salt and olive oil and with a whole bulb of garlic cut in half horizontally and roasted under it for tasty caramelised-garlic goodness, gratin dauphinois so that I could indulge my desire to peel potatoes into non-existence with my clever swivelly potato peeler (this turned out to be unspeakably tedious, though to produce potato nubs of bizarre geometric shapes; the cheese-slicing blade on the grater works better), green beans, roast butternut squash with sage. Afterwards, a chocolate pudding (standard four-ounce-of-everything chocolate cake mix, add raisins, bake in a long thin thing rather than a cake tin) served with vanilla ice cream from the shop. It was all well-received.

Now I have a large lamb leg-bone. There's clearly three sandwiches of meat on it, which can come off into sandwiches; then I have a big bone, and given bones I usually contemplate boiling them and making soup. I have carrots, parsnips, broccoli and leeks to put in soup; the caramelised garlic was so nice that I'd happily caramelise another garlic, but I'm not sure how well it works as a soup ingredient.

The last sheep stock I made was very thin and rather greasy; can I have some advice on the making of sheep soup? Something, probably one of the feasts from [livejournal.com profile] papersky's The King's Peace, makes me think pearl barley should be involved; I have pearl barley, but the pack says it must be boiled for an hour before it softens, and surely it would have to go in after the soup is blended, and at this point we'd be eating soup at ten after an evening of stressful soup synthesis.
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Third in an irregular series; last year's is here.



SLC is the Student Loans Company, to whom my debt ought to be discharged on 25th April 2008; FOREX is money withdrawn from cash machines abroad and spent, LIVE covers things from furniture to extra socks, MEDICINE is a pair of staggeringly expensive spectacles. TAX is 90% the council tax on the house I rent.

What's changed? Well, it's got a 'SAVINGS' segment this time. Food's exactly the same, rent is (surprisingly) exactly the same - I paid rent for three more months in 2007, but my brother is living with me and has paid half the rent for the last six months. For the second year running I've become proportionately meaner in terms of gifts and donations to charity; I should really do something about that.

I've spent a good deal less on entertainment, by spending a third as much on camera equipment as in 2006 and 30% less on books, though I think another component is that youth hostels in the Balkans want to be paid in cash, so come out of FOREX rather than ENT.HOTEL. I have left Cambridge much less often at weekends in '07 than in '06, though the train ticket to Istanbul meant my travel expenses were about the same in the two years.
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Beelzebub is starting to complain that his commute to the upper world is being blocked by a surfeit of countries in handbaskets.

Pakistan was clearly already balancing on the edge of its basket and waiting for a push; I'm a bit surprised that Kenya has fallen in so firmly so fast. Not a vintage year for democracy in the former Soviet Union - Georgia backsliding after a very promising start, and Russia itself displaying the tact and subtlety that has so often characterised the KGB. Ukraine muddling through.

Thailand seems to be getting out of its basket a little, though I don't know if we've seen all of the generals' response to the election results.

And most of the countries of the rich West have managed to wedge themselves sideways in handbaskets made out of inadequately-decorrelated securitised debts.

Could someone please follow up with a succession of glorious successes?
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My company decided to buy us all gym membership as a perk; the gym is conveniently located between the office, which is three minutes from my house, and the centre of town, so I really have no excuse not to go.

I was Assessed and given an exercise schedule; I'm writing it down here to demonstrate my unfitness to the gym-visiting parts of the watching world, and because it is less likely to be lost as an LJ post than as a bit of blue card in a poorly-organised box file in the gym, and in the hope that I might be able to look back in December next year and marvel at how small the weights I could lift in 2007 were, and with how few reps.

Exercise schedule )

Running on the treadmill makes my knee hurt within a minute; walking on the treadmill, or using the elliptical machines or the stepping machine, makes me sweat, and my heart rate rise from 140 to 170 over ten minutes, but my knee's OK.
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I have pillaged John Lewis, put Sainsbury's to fire and the credit card, and run amok through Lakeland.

And ended up with a bread-maker (which has made me a loaf of nice bread), a large blender (though my brother points out that soup recipes requiring long preparation and special equipment, and at the end of which you inevitably have soup, are probably not his thing), and a splendid chrome-wire flat-pack mathom stand.

It's quite a clever design; there are sixteen lengths of solid chromed pipe, threaded at both ends and equipped with deep grooves at regular intervals which are neither an inch nor 25mm, which you screw together into four side-pieces. You slide the seven baskets onto these side-pieces. To hold them on, there are twenty-eight slightly tapered plastic bits, which come in two parts that clip together, and which have ridges on the inside which click into the grooves; the cylindrical sections at the edge of the baskets are wider than the top of the taper and narrower than the bottom, so slide on and are held solidly by gravity.

On the top shelf, mathoms made of textiles. Then gym kit. Then my disconcertingly large collection of external hard disc drives (unused). Then a couple of desk-tidies filled with Miscellaneous Stuff (batteries, a complicated wire-stripping tool, a set of theatre gel samples, a Barlow lens) and surrounded by Miscellaneous Stuff comprising mostly adaptors for using English plugs in foreign parts and foreign plugs in England. A shelf of cameras, a shelf of extra lenses of moderately inconvenient size for cameras, and a shelf for flat paper mathoms at the bottom.

Soon I can get rid of the large and ugly table that I used to keep my computer on, and then used as the base for a substantial collection of intimately-mingled mathoms and trash; the mathoms are in the mathom stand, and the trash in the recycling box. I always feel a little guilty disposing of paper Economists, but the Economist archives are on line.

A question for the domestic: if I have cushion covers which measure 40cm square and 45cm square unstuffed, how large should I buy the cushions to put in them?

Christmas!

Dec. 25th, 2007 06:42 pm
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I bought my father the collected works of Jake Thackray and a Swiss Army oval water bottle in blue-anodised stainless steel; I bought my mother the six-hour Pride and Prejudice and Michael Palin's New Europe on DVD, and the book that I thought she'd like best of all that caught my eye across all the fiction shelves of Borders - unfortunately I've forgotten the title. I bought my housemate-brother Ben a pair of purple slippers and a horror movie about giant man-eating leeches from outer space; I bought my uncle Philip and aunt Eleanor the Lonely Planet Guide to the Middle of Nowhere; I bought my brother James and his wife Marian the promise of dinner at one of Cambridge's nice restaurants of their choice. I bought grandma a big box of Swiss chocolates. The links are for more information; I bought all these in real shops in Cambridge.

Mum and Dad bought me a wonderful rucksack that comes in two parts, and has straps and buckles enough to be resistant even to the baggage-handling on Ukrainian buses. Philip and Eleanor bought me goodies from Orkney, including a bottle of 14-year-old whisky. James and Marian bought me a nice bottle of Sauternes. [livejournal.com profile] bugshaw bought me a bar of tea-flavoured chocolate. And Ben bought me a hatstand.

I was silenced with admiration, and still have a silly smile on my face; nobody's ever bought me a hatstand before. It is of beech-wood, nicely turned, holds six coats, six umbrellas, and either six hats or six more light coats, and was wrapped in enough bubble-wrap that, should I ever be in the position of putting Belgium up for sale on ebay, I will have no trouble packing it.

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I've played, with great enjoyment, graphical adventure games from Day of the Tentacle to Discworld Noir, by way of Grim Fandango and Curse of Monkey Island. Are such things still made?

A cursory look around GAME at the weekend failed to show me any games of that form, and I couldn't even work out what there was that would be a single-player first-person not-pure-shoot-em-up game with a plot - Little Big Adventure, Flashback were ones of those that I liked, in what is I fear now the far past. Half-Life 2 had too little plot and too much shooting for my taste; Oblivion sounds as if it might appeal, but I've often had trouble finding the plot-line among the universe in that kind of free-flowing RPG, and got bored. I might well like a big-world lots-of-little-missions game, if any existed with a more pleasant world-view than the GTA series or Canis Canem Edit: do they?
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December 12 21:15 December 16 23:10


The hard bit is pointing the camera at the right anonymous group of faint stars that the asteroid you're looking for was near last time. Mars is much easier to find, being the brightest object in the sky except the Moon; at the same scale, and over the same time period, it moves a good deal further than Ceres did, confirming that Ceres is further away.

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Here are two pictures of the same region of the head of Cetus, taken a month apart





November 12 December 12


You will see with the eye of faith that, not only have the stars moved relative to the tree, but one of the stars has moved relative to the rest of the stars. How on Earth Piazzi managed to spot that in 1801, without the benefit of photography and not even sure that it was there to be found, I know not; I knew the asteroid was somewhere near the head of Cetus, and it still took me some time to see the blinking dot after I'd lined up the images.

Comet Holmes is still up there, it's expanded a bit, moved out a bit past the α Persei cluster, and the tail is a little more visible. Click for bigger colour image, but be warned that the sky from central Cambridge is very bright orange.


Images with the asteroid marked )
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When seeing Starlight with [livejournal.com profile] despotliz a few weeks back, I saw a trailer for The Golden Compass, and thought that the CGI (particularly the running armoured-bear scenes) looked sketchy and unfinished and poorly-blended with the background, and that this would make me very annoyed watching the film.

I saw it with my brother Ben this evening, and the animation is now finished, blends nicely, and isn't distracting at all. I think I had the same problem with the trailer and satisfaction with the film with Fellowship of the Ring.

I know film-making is the art of pushing deadlines to the absolute limit, but I don't see that producing a trailer with low-quality animation is the right trade-off to make - it's designed to show off the film in sixty seconds, for visual-effects-driven films it must make sense to show off the visual effects! At least this film wasn't proceeded by one of those ninety-second spork-gougingly tedious 'don't steal movies' adverts.
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I am sure there are those among my readers who can spend a happy hour with

http://www-cs-faculty.stanford.edu/~knuth/fasc1a.ps.gz

which is a write-up, in Knuth's inimitably erudite style, of most of the field of bit-twiddling. Highlights include a data structure for addressing the hyperbolic plane based on arithmetic in base minus-phi, and some very non-obvious algorithms for processors with arbitrarily wide words.

He recommends that processors should include the instruction MXOR, which views its two inputs as 8x8 matrices over GF(2) and multiplies them.
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This is the kind of region in comparison to which the middle of nowhere is a cosmopolitan metropolis.

It's on the south coast of the south-eastern tendril of Papua New Guinea, in the province of Milne Bay which you will not have heard of, roughly between the towns of Abau and Alotau which you will not have heard of. Probably easiest reached by a two-day trip in a medium-sized boat along the coast from Port Moresby, though there may be pirates. There are bits and pieces of roads, but the rivers are big enough that they don't seem to be bridged.

I think this is an oil-palm plantation, and I think the ten-metre-wide tin huts on 25-metre centres are the houses of the workers. Each medium rectangle is a twelve-hectare plot. As you scroll around, you'll find lots of other large patches of land nearby set out as demonstrations of different kinds of graph paper.

I get lost in Papua New Guinea merely scrolling over it in google-maps; I dread to think what it's like on the ground.

I'm surprised quite how much of PNG has images at one-metre resolution; maybe there's an NGO out there interested in deforestation and with a large IMINT budget. The satellite imagery pricing I can find on the Web is $8000 for a single picture of 272 square kilometres at three-metre resolution.
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This isn't a ship going through icy water; it's the wake in the clouds where the Roaring Forties hit Bouvet Island, a medium-sized volcano conveniently located a thousand miles from one of the less-visited parts of Antarctica.

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Walking back from town, I bumped into [livejournal.com profile] j4 on her way to sing carols in the craft-market opposite Trinity chapel; I wandered along, met the choir, discovered it contained [livejournal.com profile] pseudomonas and a number of other people that I vaguely recognised, and was convinced to help out by shaking a collecting tin. Indeed, two collecting tins.

Collecting tins, it emerges, make superb maracas; you get the drum-roll effect from shaking them side to side, various volumes of cymbal-like clash by shaking them up and down, and since there are slots in the base for your thumbs, you can slam them together quite hard to get a different range of percussive noises without risk of crushed thumb. 'Wassail, wassail' and 'Rudolf the Red-Nosed Raindeer' are particularly amenable to percussion accompaniment.

A really rather good four-part choir accompanied by a dancing lunatic playing percussion parts on the collecting tins turns out to make quite a lot of money; I suspect at least a hundred pounds ended up in the maracas by the time they stopped singing at 3:15, and it'll all go to the local childrens' hospice. After tea and treacle tart in Tatties, my fingers defrosted without further issue.
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Halifax will sell me a 3-month bond paying 6.85%, a 6-month bond paying 6.5%, a 1-year bond paying 6.45%, a 3-year bond paying 6.4%, or a 5-year bond paying 6.2%.

I thought that longer terms were supposed to be rewarded by better interest rates; on the other hand, why shouldn't I jump at this?

If I assume that Halifax would rather borrow money on the money-markets, where LIBOR is 6.61%, than through the time-consuming process of assembling small sums from thousands of tiny savers, then I conclude that the money markets want to charge Halifax perceptibly more than 6.85%. I think that this means that they believe there is a chance of perceptibly more than 0.89% [(6.85 / 6.61) ^ (3/12)] that Halifax will be unable to repay.

On the other hand, I'm a small saver, and the regulatory framework likes small savers. If Lloyds lend Halifax fifteen million pounds, and Halifax goes bust, Lloyds get nothing back. If I lend Halifax fifteen thousand pounds, and Halifax goes bust, I get £13,700 back. So I should be more willing to lend Halifax money than Lloyds is - indeed, since the money is otherwise making 5.8%, I should lend it to Halifax if I believe the odds of Halifax still being around in mid-February are better than about 20:1 for.

This seems somehow counter-intuitive; on the other hand, I will go off to the local Halifax tomorrow with a chequebook. There is then the question of hedging: I wonder what odds the local Ladbrokes will offer on Halifax being bust by mid-February?
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It takes about an hour and a quarter from the time the heating turns off to the point that the house is cooling to the stage that you might want to be lying under a warm duvet and a blanket.

It takes about an hour and a half from the time the heating turns on to the point that the house is warm enough that you can bear to get out from under your warm duvet, and retrieve the blanket from down the side of the bed where you've kicked it.

So, heating should come on at 0700 and off at 2200, and I might end up with something that you could confuse with a sleep pattern if you held it upside-down and squinted.

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