Monday, January 20, 2014

tug of war

For months now I have been awaiting the outcome of the ping-pong between my boss and the guy in Beirut who sent us 250 samples to analyse. I'm sure I blogged about that project, but it's been a while. Anyway, the bossguy wants the results to be presented to the patients the way we would present them to our patients - with a real results sheet, interpreted and signed by the lab experts.
That means having the name of the patient on the report, as well as other usual identification details like their date of birth and sex.
But the other guy, he's got a research project going. What is it to us what the samples are called? None of our business. Anonymisation in research is a good thing.
Well, sure, and if we're just going to send a table back to Beirut with a mutation attached to a sample code, and that's it, ok. But one of the things our southern collaborators are bugging us about is the analysis taking so long while the patients are waiting for their results. And if the patients are waiting for results from us, we want those results to be as proper as possible.
No, no, the Lebanese want to take responsibility for getting the right result to the right patient. Just write a report with the code, and they'll add the name.
Doesn't work for us. No names, no reports.

I've had the bulk of these reports ready since October, waiting for the back and forth to end.
In the meantime, we have had to give them summary tables of our progress, in order for them to show their financial backers some progress, and to allow presentations and papers to be prepared. For us, these were strictly research-use results, but of course they went back to their patients with the information. So instead of getting a report where the results are interpreted and put into context by cancer genetics experts with recommendations about how to proceed, they got the bare bones.
Who comes out ahead there?
I don't know what they did with some of the stickier results, the "unclassified variants", but over the holidays we did at last receive a table with names across from the codes.
Of course, they put the whole name in one column, so you have to guess what's the family name, what's the given name (in your own culture that seems obvious enough, but to me, Majed and Haroum and Issa could go either way). Plus, most were 3-part names, and it isn't clear if the middle one is a person's middle name (second given name), or if it's a 2-part last name, or a maiden name. So I was not well advanced by that.
Turns out, the second name is the given name of either the woman's father or her husband. OK. It's still unclear to me if that is a usual way of referring to people in that part of the world, or if it's just the way their computer has them listed (as indicated in a semi-explanatory email).
This is all I'm going to get, however, for the identification of these cases. Birthdate, forget it. Sex I can verify on the pedigrees.

The boss is satisfied to write the reports now.
What I'm still not convinced of is whether we are actually more certain now that the right report is going to the right person. All I've done is taken a name from a list and added it to my report, which was generated according to the code. I will have someone check that I haven't made any mistakes (yes, you're welcome Yannick!), but how do I know the list is right? That there wasn't some mixup in the codes?
It is good to have a report with a name on it.
But is it really more secure for me to add it than for my collaborator to?

Wednesday, January 15, 2014

Last day in England

Our last day in England we spent bumming around the house, and going shopping at Morrisons for all sorts of goodies you can't find in Nowhere France. Cheddar cheese. Drambuie. Lime marmalade.... At the shop we picked up our only real souvenir of the trip (aside from the memories and photos, and the books are only mine so they don't count), a pair of porcelain coffee cups in blue & white patterns.

Not much to say, just "oh, look!! another tree I saw while on vacation!!"

And, "oh, look!! People walking their dogs!!"

 Alright, I'm done being snarky. It's time to go home for dinner anyway.

Tuesday, January 14, 2014

A spot of sun

Friday morning was so dreary we concentrated on being happy it wasn't worse. Back in London proper we walked around for a while, and miraculously, the sky cleared up. Just for an hour before the sun set. The kind of thing that makes you think - dang! if only we'd stayed longer in Greenwich, we could have nice pretty photos instead of dark & cloudy ones! Is it too late to go back? We have ride-all-you-want tickets...
But nah, strolling around the Tower Bridge area was enough. I like the contrast between the old and new in the area.

Monday, January 13, 2014


Friday we went into town again, this time on the train. I was happy to take the train because it meant I would get more walking in than we would with the car, though I did have to remind myself to proceed at a pace more convenient to my companion. Don't want to burn him out on walking around!
We went down to the station with Jean-Philippe's son Philippe, who was headed in for a day of work so we left quite early and had the benefit of his knowledge that if you change two stations down the line you'll get there much faster because the new train is direct to London Bridge instead of making every little stop on the way. A lot of people seemed to know this, and indeed, when we got to Greenwich after two more changes the world was still just barely waking up. Rather like in France, anybody who could had taken the rest of the week off, and the rest were not too happy about having to get up in the morning.
With nothing but the coffee shops open yet, we stopped breakfast at Starbucks before walking around this nice little town. Most of the place seems to be taken up with museums & historical sites, and the bit of town left, at least in the center, is mostly tourist shops and restaurants. The Cutty Sark is here, up on blocks with its museum underneath.
As you can see, the weather was quite threatening. I had my anti-rain device with me, and I choose to believe it saved us from worse. There were no ships of interest dockside, and the view along the Thames was quite dull. The poor light didn't help, but the riverfront is not much of an attraction.
At the University of Greenwich, we wondered what this apparently recently delivered statue could be. Or recently renovated, given the plinth is not exactly new. Turns out it's King George II, wrapped up for the winter as usual. We decided not to wait for the unveiling.
They have some spectacular facilities there at the U of G. Like this chapel (sorry for the uncorrected color balance - the ceiling is a gorgeous blue and white in person)
Across the quad, the dining hall is a mirror of this room, with its own set of fantastic paintings. Set to seat hundreds, I wonder if the food is as sumptuous. Or if the decor serves to distract. Or if the quality of life is some kind of average of all the things in it, and so if you're really pampered here, it's got to sting there...
Onwards. At the Maritime Museum across the street, we again don't go in. It seems all the signage is in English, and JP isn't interested enough to have me translate everything. Though surely they have audioguides. No, really, it's not worth the entry. (We kind of go back and forth on this, because I'm not that interested either, but we did come all this way, and I thought because he was interested...) So we just look at the stuff outside. There are some Works of Art. I declined to photograph them. At the far end of the very large lawn, there's a collection of cannons and anchors, all in standard black, and an intriguingly colored item.
A drill head, ah.
Major drill!
Can't go to Greenwich without seeing the Royal Observatory and the Meridian Line.
No, really, you can't. It isn't even 10:30 am yet, and we cannot possibly pretend to wander about the village until lunchtime without going into some museum, and my companion nixes walking up and down the hills of the park just for the fun of it. The park is quite grand, and would be much improved by a bit of sun, but in spite of my (admittedly puny) anti-rain device we prefer to stay closer to shelter. Besides, I really must see what sort of marker they've come up with for the meridian.

Oh, look, a picture of a tree I saw on vacation!
Yes, but it is a special tree. I didn't see any particular plaque associated with the tree (though, honestly, I didn't think to look until just now - if there was one, it didn't capture my attention at the time), but it gets to be photographed endlessly as the Tree at Greenwich Observatory. And it's a pretty nice one.
Some kind asian tourists agreed to take our photo with the meridian thingy.
JP thought they must be finished already & so started to walk away. Then it started to rain again, so I just recovered the camera and that was it. By the time I finished with the Observatory, it was a decent hour for lunch, and we descended the hill in the drizzle looking for a nice curry but that place was closed so we settled for a nice pub serving fish&chips and burgers with onion rings. That was right next door to a charity shop selling books, where I picked up book #19.

Saturday, January 11, 2014

bumming around London

On Boxing Day we went into London by car because the trains weren't running. Strange they would just shut the suburban stations like that. Dec 26th isn't a real holiday. It's just a day people like to have off, and it's become a tradition. No train service? The heck is that? How will people get to the shops??
So we drove, which wasn't too eventful. Only a few wrong turns on the way home because the gps doesn't have time to read out the road name before you've missed it already, in the twists and turns downtown. And the screen is so small it's hard to tell if it means turn right now immediately, or a couple meters on. Personally, I prefer to take a good look at a good map before setting out, and not to have the thing on if one can help it. But when there's lots of turns and one-ways, it's useful.
When we got to Waterstones it was closed, though there were people messing around in the windows. It was after 11 already so I figured they'd be open if they were going to open, and we went to that other huge old bookstore down the block instead. They were open. They sold me a dozen books, and it could have been many more but we were hankering for lunch. For a while I alarmed JP by accumulating a huge pile, but I trimmed it down before heading to the register.
Lunch was nice except for the now-repeated experience of JP's bank card not working. This was the maybe the fourth time, though he always eventually found an ATM that would take his card. I had some problems with mine, too (though not at the bookstore!). It's better to withdraw a big chunk of cash anyway, because below a certain sum the minimum transaction fee is more than the % fee for larger amounts. And I find counting out cash keeps my spending in check.
Once fed, we strolled around the parks and had a look at Buckingham. 
The weather was iffy. We had the good luck not to get rained on, and the sky was often interesting. I can look all day at bare trees against the sky. It's the stark silhouette of the branches, so solidly black and intricately complicated, all form and no color, against the delicate changes of blue-white-lavender/grey in the sky, all color and no form, that captivates me. 
I took a couple of shots, including this one, and some 20-something American walking with her friends behind us started going on about how stupid it is to take photos of some random tree in a park while on vacation. 'Oh, look, here's a tree I saw in London!' 'And look! Another tree!' 'Gee, how dumb is that, to take such boring, dumb pictures!'
I don't mind people not being able to appreciate the same beauty that I do. But it does embarrass me to be an American sometimes, knowing there are so many of this kind of jerk walking about loudly dissing what isn't any of their business at all.
 Oh, look, another photo of a building I saw on vacation. Does the flag mean the Queen is In?
 Frankly, I find the trees much more interesting!
 Oh, look, another building and a statue I saw on vacation. Winston Churchill, of course.
 St Mary's with Tree.
And lastly (for today), the backside of Parliament.
After that it started getting dark, so we had a coffee and wandered back towards the car. Waterstones was now open - Yea!!!- so naturally I just had to stop in. Just six books this time. With the pile I'd made previously, I often wasn't sure whether a particular volume had made it to the register at the other shop, and it's silly to buy duplicates - not like I can just pop back and exchange one easily. As it turned out, all 18 books for the day were unique. I'm set to read for a few months.

Friday, January 10, 2014

Heading North

Before it becomes an entirely different holiday season, let me show you around our Christmas vacation.
Yes, I know. My head must be tilted. I cannot for the life of me spontaneously take a photo with a level horizon, and even when I pay attention they come out a bit wonky.
This is Boulogne sur Mer, on the Channel coast where we stopped for the night, having driven across France in a drizzle. Right when we got off the freeway it started raining for real, and we considered ourselves quite brave to take a stroll up the boardwalk to the center of town.
So I took these in the morning, while Jean-Philippe strapped the table top back to the roof of the car. It is our mission to deliver this table to his son, who lives near London.
To cross the water, we took the shuttle through the tunnel. There's a huge parking lot & shopping center for your amusement as you wait for your train, but there weren't many people that morning, and the train before ours was far from full, so they let 'N' train people board the 'M' train. Just drive right on board.
You can get out of your car in the shuttle for the 20-odd minute trip, but why bother? Don't stand between cars, in case somebody didn't set their brake and there's a hic. There is nothing to see. You can't tell how fast you're moving, or how far you've gone. They tell us our average speed is more than 160 kph, which means our top speed must be quite a bit more. You don't feel it at all. Just eventually there's an announcement and they let you out, and you have to drive on the left. Fortunately, there are lots of directions and 'wrong way's painted on the ground.
Once in England, we have a GPS adventure. Typing in the address and not just the post code, JP's phone sends us toward London, fine, then through the heart of the city on surface streets which was a surprise, and finally to a destination in Chiswick or somewhere on the north side with nothing to do with the place we wanted. Idiot thing. We phone Philippe and are told to enter just the post code, which in the UK only refers to a handful of houses or even just one. That gets us to Kenley on the south side of London with no further problem.

The rain continues, and becomes quite serious overnight. By morning it clears up somewhat, but the countryside is so waterlogged you need rubber boots to go hiking at all. I don't really care about mud on my shoes, but JP is much more fastidious. 
Trees are down everywhere and there's a problem on the rail line to the city, so JP and I just wander around the next door town of Purley for the day. Not much to see in Purley, but we stretch things out until a decent time for lunch in a pub, having such classic English fare as bbq pork ribs and steak with peas, with pints of Guinness or cider. There is no bookstore in Purley, I notice, but we will be going to the City another day.