Tofino reprise

Last week, I was away on vacation, capping off my month of not being around much.  And what a month it has been!  The final week of June was spent about as far west as you can get in Canada with a car.  It is, in fact, the western end of the trans-Canada highway.  Which, if I may say so, just kind of ends on a little unobtrusive dock.  Highly unimpressive.

Anyhow, my wife and I convinced my parents to join us out there to enjoy some great food, beaches, scenery and (of course) company.  We all had a great time, and my wife and I even took a surfing lesson on the one least rainy day. (She still has the bruises, but I guarantee I drank more salt-water.)  In any case, I thought I’d post one of my wife’s pictures – One of the few times I’ll let anyone take my picture, really – I’m far from photogenic.

Although you can’t tell from the picture, all of the rain gave me the perfect opportunity to show off my Complete Genomics hat.  I’ll go out on a limb here and suggest I may have been the only person in Tofino (pop. 1,650) who had the faintest idea what Complete Genomics is, but that isn’t quite the point.

Anyhow, with the weather being so un-cooperative, I don’t have much in the picture department to show.  I’ll just include my favorite of the trip – part of the broken islands.

I’m glad I had the chance to visit Tofino in the summer – it’s really a stunning place. Hopefully, one day I’ll visit and witness a day when it doesn’t rain.

Just to close out, I have two pieces of advice:

  1. Surfing in a wet suit isn’t nearly as bad as it sounds – the water is warmer than it looks.
  2. Don’t give your kids a DVD player to watch on the road to Tofino, there are a lot of mountain switchbacks, and carsick kids can be messy. (Passed along by a colleague of my wifes, but the advice sounds pretty good!)



Looking for advice on moving to Europe

My wife and I have seriously been contemplating the future.  With the figurative grad school light at the end of the tunnel being visible, if not quite in focus yet, we’ve been seriously considering an opportunity to move to northern Europe.  (Yes, I’m being as generic as possible.)  However, neither one of us have lived outside of North America –  and have only visited Europe a couple of times on vacation.  That makes it pretty hard for us to critically evaluate the opportunity.

Thus, crowd-sourcing!   I was wondering if anyone had any advice they might be able to share with us on what we can do to make that move successfully – both things we should or shouldn’t do.  Or, if people think it’s a great idea, or a bad idea.  Really, we’re trying to cast the net as wide as possible on whatever advice people can give us because it’s really hard to make a decision like that without talking with people who have done it.

Some of the outstanding questions we have:

  • How did you find the language learning curve when moving to a non-English country?
  • How much of your stuff did you take with you?  What did you do with the stuff you left behind?
  • How did you find solutions to the “2-body” problem?
  • How long does the culture shock last?
  • Was it a hassle bringing pets?
  • What are the big “gottchas” that you didn’t see coming?
  • How long did it take to organize your move?  How hard was it?
  • Would you suggest that other people do it?
  • How long did you stay? (yes, not leaving ever is also an acceptable answer.)

And, of course, are we even asking the right questions?

Any advice you can give would be helpful for us, and of course, for other people who are faced with this decision in the future.


Phoenix, Arizona

I’ve only been in Phoenix for a few hours, but I’ve had a chance to form a few impressions that I thought I’d share.  Unfortunately, I didn’t bring my camera as I didn’t think I’d have the opportunity to take any pictures, so unlike my visit to Copenhagen, my description will have to be entirely verbal.   In any case, I’ve had a couple of unexpected hours to wander the streets and learn a few things.  None of them are complaints – but they’re all things that really stood out for me this evening.

First, you don’t sweat in Phoenix.  Sure, your body might try, but the dry desert air sucks the moisture off of you so fast that it doesn’t have the opportunity to accumulate.  In fact, it sucks the moisture out of your pores, sinuses and throat too.   Oddly enough, you don’t really notice until you walk past a restaurant that is sprinkling cold water onto it’s patio as if it’s guests were ferns.  At that point, you notice how dry everything else is – and realize you should have packed an extra bottle of water when you went out walking.

Next, the vegetation in Phoenix’s downtown core is out of this world.  Nothing here grows in soil – anything that isn’t paved is covered in crushed red rock, out of which spiky cactus, succulents and whip-like grasses form tufts of green (or yellow) that look positively Martian.  I did find a strip of what was probably grass, once upon a time, but even that was growing (or had been trying to grow) out of a patch of crushed red rock.

The city is scattered with art, perhaps to made up for the sparseness of the landscape.  My favorite looked to be a 5 story tall net and metal “thing”, suspended above a parking lot, which was sort of reminiscent of what it would look like if you crossed a jelly fish’s dome with a mobius strip, flipped it inside out – and then made it out of enough mesh to shield a small african nation from mosquitos.

The building are tall, straight… and brown.  Actually everything is tall, straight and brown – or some shade between beige and red.  Coming from Vancouver’s green glass landscape, the red somewhat sears the eyeballs.  Everything from the soil to the bike racks to the entire face of a 30 story building are all painted or designed in a desert landscape palette.   You really can’t forget you’re in a desert when you’re in Phoenix.  (Even if the constant barrage of cacti weren’t enough.   For the record, I’ve always been a big fan of cacti, ever since I was a child, so this really isn’t a complaint!)  Even the architecture reminds me of cacti – either tall and narrow, or squat and boxy.  I propose that desert architects are probably inspired by the limited vegetation.

The days are short in the summer.  This is not a bad thing, really – the sun is seriously bright and hot in Phoenix, and I probably got more sun in 3 minutes here than I did all of last year.  However, I was surprised to see darkness descend at 7:30pm.  Summer days in Vancouver, for comparison, stay bright at least another 3 hours.

Finally, downtown Phoenix is pretty empty on a Sunday night.  That probably doesn’t surprise anyone, however.  I’m used to seeing tons of people out and about on in the summer time, enjoying patios and the good weather.  I suppose when your good weather never ends, there’s just that much less pressure to make the best of it.

All in all, it’s really a pretty place – and I’m glad I’ve had the chance to wander around a bit.  And, for the record, they do really good calzones here. (=

Copenhagenomics 2011, in review

It’s early Saturday morning in Copenhagen and Copenhagenomics 2011 is done.  I was going to say that the sun has set on it, but the city is far enough north that the sun really doesn’t do much more than sink a bit below the horizon at night.  That said, the bright summer sunshine has me up early – and ready to write out a few thoughts about the conference.

[Yes, for what it’s worth, I was invited to blog the conference so I may not be completely impartial in my evaluation, but I think my comments also reflect the general consensus of the other attendees I spoke to as well.  Dissenters are welcome to comment below.]

First, I have to say that I think it was an unqualified success.  Any comments I might have can’t possibly amount to more than suggestions for the next year.  The conference successfully brought together a lot of European bioinformaticians and biologists and provided a forum in which some great science could be shown off.

The choice of venue was inspired and the execution was flawless, despite a few last minute cancellations.  These things happen, and the conference rolled on without a pause.  Even the food was good (I didn’t even hear Sverker, a vegetarian Swede, complain much on that count) and the weather cooperated, clearing up after the first morning.

As well, the conference organizers’ enlightened blogging and twittering policy was nothing short of brilliant, as it provided ways for people to engage in the conversation without being here first hand.  Of course, notes and tweets can only give you so much of the flavour – so those who did attend had the benefits of the networking sessions and the friendly discussions over coffee and meals.  The online presence of the conference seemed disproportionately high for such a young venue and the chat on the #CPHx hashtag was lively.  I was impressed.

With all that said, there were things that could be suggested for next year.  Personally, I would have liked to have seen a poster session as part of the conference.  It would have been a great opportunity to showcase next-gen and bioinformatics work from across europe.  I know that the science must be there, hiding in the woodwork somewhere, but it didn’t have the opportunity to shine as brightly as it might have.  It also would have served to bring out more graduate students, who made up a small proportion of the attendees (as far as I could tell). Next year, I imagine that this conference will be an ideal place for European companies and labs to do some recruiting of young scientists – and encouraging more graduate students to attend by submitting posters and abstracts would be a great way to facilitate that.

Another element that seemed slightly off for me was the vendors.  They certainly had a presence and were able to make their presence noticed, but the booths at the back of the room might not have been the best way for companies to showcase their contributions.  That said, I suspect that copenhagenomics will have already outgrown this particular venue by the next year anyhow and that it won’t be a concern moving forward.

While I’m on the subject of vendors, what happened to European companies like Oxford Nanopore, or the usual editor or two from Nature?  Were some UK attendees scared off by the name of the conference?  I’m just putting it out there – it’s entirely possible that I simply failed to bump into their reps.

In any case, the main focus of the conference, the science, was excellent.  There were a few fantastic highlights for me.  Dr. John Quackenbush‘s talk challenged everyone to seriously re-consider how we make sense of our data – and more importantly, the biology it represents.  Dr. Elizabeth Murchison‘s talk on transmissible cancers was excellent as well and became a topic of much conversation.  Heck, three of my fellow twitter-ers were there and each one did a great job with their respective talks. (@rforsberg, @dgmacarthur and @bioinfo)

In summary, I think the conference came off about as smoothly as any I’ve seen before – and better than most.  If I were given the opportunity, this would be a conference I’d pick to come back to again. Congratulations to the organizers and the speakers!

New ideas

It’s 6:00am, with three hours before Copenhagenomics and I’m solidly awake.  Jet lag is annoying, at best, but it’s been a great week of travelling and visiting in Denmark.  The interesting thing for me has been how stimulating it has been as well – even before the conference has started.

Part of that has just been getting myself out of the thesis mindset.  I’ve gone from being focussed on wrapping up my project to thinking a little further out.  That is, what would I work on if I were not summarizing my past work for my thesis. It was a question put to me by a bioinformatician at CLC bio, and I like sore tooth, I just can’t stop playing with it.

Because of it, I’ve come up with some wonderful ideas.  I guess this, to me, is just reinforcing the idea that sabbaticals really do work.  Even if the break from writing is short, just breaking out of the artificial walls I’d built around myself to keep myself from getting distracted from my thesis and papers has been a productive change.  Interacting with new people has been a great catalyst.

I’m really looking forward to the conference this morning and the opportunity to interact with more people and spark even more new ideas, but now I’m also looking forward to going home and getting my thesis done.  I have things I want to do and all this writing is standing in the way.

Copenhagen/København – 1 day before Copenhagenomics

Copenhagenomics starts tomorrow, and I’m getting excited.  I can’t wait for it to get underway.  I’m finally over my jet-lag, and looking forward to some good science talks.

That said, I still spent today walking copenhagen until my feet hurt!  We managed to see the round observatory tower, Rosenberg castle, the Danish crown jewels, the residences of the Danish royal family, the Danish Aquarium and the Zoo.  How’s that for a full day?

Anyhow, like yesterday, I have some pictures to share with you, so if you can’t be here for the conference, at least you can feel like you’ve visited some of the city.

For the record, the Danes are pretty touchy when it comes to their jewellery – I managed to get scolded for touching the glass while taking pictures (after paying the 20kr for a photography permit, I might add), and my wife got a loud “HEY” from an armed guard for standing too close to his shelter.  An exciting day, all in all.


While my laptop is perhaps recovering from whatever it didn’t like about the flight (I got it to turn on, but the screen remains black), I’ve been helped by some fantastic people at CLC bio, who have lent me a spare linux laptop. (It actually says “Spare Linux” on it.)  They have been incredibly kind to me this week, and even took some time to give me a tour and tell me a bit about their work.  While I don’t plan to blog about that specifically, it’s clearly worth a mention.

In any case, I thought I’d put the laptop to use and post a few photos I took today, as well as a few from sunday.  (I put away my camera yesterday, so there are no pictures to share from the Århus trip – and yes, I was just looking for an excuse to slide an å into this post somewhere.)  The pictures are pretty amateur (apparently jet lag isn’t good for working out composition), but they give a flavour of the city.

Copenhagenomics, here I come

In 24 hours, my wife and I will be boarding a plane for Toronto, to start our trip to Copenhagen.  I’m incredibly excited and have been looking forward to this since the invitation to go out that way arrived.

Unlike other trips out of Canada that I’ve done, this one is mostly about business.  I’m surprisingly excited about being an official conference blogger – that’s an experience that I doubt many people have had an opportunity to try – and I’m all ready to give it a shot. (I’ve even downgraded the kernel on my laptop to 2.6.37 to try to extend the battery life, just to get an edge on computer time between charges – how’s that for nerdiness?)  Copenhagenomics is looking to be an awesome conference, and the organizers are doing a great job with the web page, building some of the suspense for me.  I’m anticipating a great time – and a lot of “instantaneous blogging”.  (It’s one thing to write posts and sit on them for a few hours, and another to post blogs as an event is in progress.)

I’m also not going to pretend I don’t have other reasons to be excited.  I’m really looking forward to doing some photography in Denmark.  I’ve got my camera all packed up and ready to go, although I’m only bringing my stripped down gear: one body and two lenses.  I don’t expect to do a lot of photography during the conference, but we’ll see how it goes.  I’m not bringing the outboard flash, tho, so no conference party pictures, in case anyone was worried.

I’m also going to visit CLCbio, which I’ve been looking for an excuse to do for a long time.  If you’re not familiar with them, they’re one of the best independent bioinformatics/nextgen companies around, and only a train ride away from copenhagen.  I had seriously considered moving FindPeaks to their platform at one point, but in the end, decided it was a project that wouldn’t work towards my thesis – but I’m still excited about the platform and learning more about the company.   As you can imagine, I won’t be blogging this part of the trip, but it’s one of the standout highlights we have planned.

Finally, there’s also Copenhagen itself.  I’ve never been to Northern Europe, so it should be great fun.  Obviously, I don’t speak danish, but it’ll be fun to learn a little while we’re there.  I always try to pick up a few native words wherever I travel to somewhere non-English speaking. (My favorite word from our Tahiti trip, by the way, is Moh’oh’poh’pah’ah, which means frog.  I don’t get to use that in conversation often enough, so I thought I’d slip that in here.)

Oddly enough, I’m also looking forward to the plane ride itself.  Given 5 hours and 8 hours of travel time on the two legs, in which I’m stuck in about 1 m^3 of space, I figure I should be able to work on my paper/thesis without any interruptions.  With some luck, I’ll be able to finish off the paper, and maybe toss in a few pages of Chip-Seq discussion into my thesis.  Good times.

In any case, this should be a fun and productive trip.  Now, if you’ll excuse me, I have to go stuff a few socks into my bag.  See you in Copenhagen!

Vacation time…

So, Today’s blog is a little bit different. First, I’m not going to do any serious blogging – I have lots to add to the conversation about indels yesterday, but I’m going to have to leave it for a while, and come back to it in a few weeks. After all, I have a few other things on my mind. I’ve been planning a vacation with my girlfriend for the past… oh, say… 6 months – and it’s finally arrived.

Second, I’m going to experiment with un-moderated comments – with some luck, there won’t be too much spam while I’m away. If it works out, I’ll leave it that way once I get back as well. Hopefully, that will help encourage more open conversations, as comments should appear on the blog right away.

Third, I’m just going to provide a little bit of information on how to contact me – since I won’t have email, you’ll just have to do it the good old fashioned way and mount an expedition. To find me, you’ll find several clues in the photos below, from someone who’s already returned from the trip I’m about to take. Actually, the pictures are well worth looking through, if you need a reason to procrastinate – the photgrapher is fantastic:

Link to photos

Anyhow, I promise to reply to emails, tidy up comments and all the rest of that stuff when I get back. But for the next two weeks, this blog will be quiet. Happy end-of-August, everyone, and see you in September.