Ok, you’ll never guess what I came across today!  Or, well, if you’ve read the topic, you might…  I found an (apparently) owner-less Wacom tablet.  That probably doesn’t mean much to most people, but in my experience, you don’t just find Wacom tablets lying around gathering dust… unless they’re broken of course.

So, while I was cleaning up the desk next to mine for a rotation student, I discovered it just sitting there.  I’d never seen one without a fancy engineering template taped on top, so I assumed it was either broken or missing a piece or relegated to its dust gathering status for some equally horrific disfigurement.  I cheerfully set it aside, thinking I’d just plug it in later to see why it was discarded.

Well, much to my surprise, the thing works!   If you’ve never seen a Wacom tablet before, it’s the king of mice, the grand father of touch pads, the cats pijamas.  Holy cow are they cool.  I plugged it in and started doodling with it immediately in inkscape.  Seriously, that is a nice piece of hardware.

I have the feeling that, if no one claims it, I’ll be doing some serious doodling for all of my projects – and with my plans for doing visualization work, this could be the start of some really fun images.  While I’m still feeling pumped about it, I’ll challenge myself to post something drawn with it for next week…  in 7 days I should be able to do something neat, otherwise I am clearly unworthy of such a lucky find!

Is Encode bunk?

Ok, I’m sick, so this is a very short post.  I just stumbled onto this article in the guardian.  Not being a Brit, I have no idea if it’s even a remotely reputable journal, or why this piece is so sensationalist.  So… scientists see evidence and are working to understand whether much of the genome serves a purpose and they disagree on the interpretation.  Neither side has conclusive evidence, but the Encode project certainly has evidence that makes it’s claims seem valid.

In contrast, a bunch of biologists seem to have jumped on it and insist that most of the DNA in the human genome is still “junk” and does nothing.

While I don’t support the side that seems to be calling “BS” on the Encode project, the character of the article seems unnecessarily vitriolic.  Does the UK have republicans?

Edit: Finally feeling well enough to get back on my computer and look for the source of this argument: Here.  And after reading a few pages…Wow! I can’t believe that was published as is.  The abstract alone sounds like someone got up on the wrong side of the bed, and then ate nettles for breakfast.

A few things on python

A few quick notes.  Python, so far, is really a neat language.  It’s fast to write in, it’s easy to do unit tests and using pydev made the transition to python a lot easier from Java.  I’m not nearly a professional python developer by any stretch, but I can bang out python code pretty quickly now, and I’m pretty happy.

Duck-typing does annoy the heck out of me still, because I know things will crash at run time instead of easily caught errors being flagged while writing the code or while compiling, but I’m sure I’ll get over that, and unit tests do compensate for it.

I’ve also picked up Egit for version control, and that has been a bit confusing – not because it’s git, but because the git model of software development doesn’t provide an external backup for your repository unless you push it to the server.  Somehow, I hadn’t actually realized that until I started playing with it.  It simply means pushing to a branch at the end of the day for a backup, or at stable points, which isn’t a bad idea, really.  Once I get more comfortable with the system, I’m sure it’ll work far better than SVN ever did for me.

Beyond that, I’m also pretty impressed with the libraries available for python.  I’ve played a little with Pysam, and have been reasonably impressed with the results.  I haven’t done any benchmarks on it yet, but I’m ok with it so far.  It did take me a while to realize that an aligned read’s “.aend” property is the 3′ end and the “.pos” is the 5′ end on the positive strand… and I’m not convinced that I haven’t somehow introduced an off-by one error in the code, but these things will be sorted out in time.

Otherwise, I think I can say I’m reasonably happy with the choice of python.  I’m looking forward to playing with a few other libraries, like matplotlib, and scientific python, as well as Tkinter, and – although I know there will be a learning curve on it – I think there are more than sufficient python tutorials and forums to help make it reasonably easy to get through.

Ok, time for some more coding. (-:

Technician position – Kobor lab

If you know anyone who is looking for a position as a research technician in a lab doing epigenetics, please send them this way!

While I can’t link directly to the position (stupid UBC website), I can tell you where to find the information: Click on http://www.hr.ubc.ca/careers-postings/staff.php and scroll down till you find Job ID 14939 and then click on the title “Research Asst/Tech 3”.  You’ll find something like this:

This position focuses on interdisciplinary epigenetic research in human populations as it relates to environmental exposures and health outcomes across the lifespan.  It offers a unique opportunity for somebody interested in the interface between molecular biology and various disciplines such as psychology, psychiatry, epidemiology, and child health.  This is a research position in which complex and advanced technical skills are required. Epigenetic variation will be measured using sophisticated high-throughput genomic technologies, such as DNA microarrays, next-generation sequencing, and pyrosequencing.  The ideal candidate will have the technical skills necessary to perform the measurements and the ability to learn the statistical and bioinformatics tools that will be applied to test for association between epigenetic variation and different exposure or outcome variables.

Works in an air conditioned, well illuminated scientific laboratory with adequate bench space. Possible hazards include chemicals, radiation and biohazardous materials at the bench and surrounding area.  Standard safety procedures are in place to protect the employee and minimize accidental exposure to work place hazards.

You can apply directly on the web page described above.  And, I can tell you that this is one of the most friendly labs I’ve ever had the opportunity to work with.

Q&A: I don’t really hate Danes

Just doing some housecleaning today – I don’t want this to be a long post, but I do want to clarify a few things.

Q. Do you really hate Danes?  A. No, I don’t hate Danes.   I’ll admit that I’m extremely angry at how things turned out at the end of my stay in Denmark, how the whole relocation was handled and what I perceive as a lot of untruths that were told to me.  That has significantly coloured my perception of my experience in Denmark, but no, I don’t hate Danes.

Because the lawyers are still arguing over the legality of how things unfolded, I haven’t given specifics, and won’t until it’s settled.  And those of you who think you know what happened… well, you haven’t heard all sides of the story because I haven’t told anyone.  Patience – it will likely all come out eventually.

Q. Do I think all Danes are unfriendly?  A. No, Danes are actually very friendly, and there were a few people I met in Denmark whom I would otherwise have wanted to keep as friends.  I’m sure those people know who they were, as they were mainly the ones who made an effort to speak in English when I was in the room, or even to start a conversation with me.

On the other hand, I can’t tell you how many times people would bump into you while walking or jogging, despite trying to move out of the way, or the thousands of other little things that are probably normal in Danish society that frustrated the hell out of me.  Certainly if someone bumps into you on the street in Denmark, you shouldn’t expect them to acknowledge it, let alone apologize.  It is perfectly possible to be a friendly person, and yet still, as a culture, be unwelcoming.

Q. Do I think Danes are unwelcoming? A. Well, Yes – but as I’ve said, not individually.  As a society, they’ve geared things to be very smooth for people who are citizens and know the system, but to be a little more jagged for foreigners. I won’t tell other people’s stories, but I met perfectly decent people who’ve been in Denmark nearly all their lives (20+ years) and are still waiting to become citizens or are fighting with the paperwork.  Danes’ views on foreigners are clearly dependent on where they come from, and interacting with the bureaucracy can be challenging for someone who doesn’t know what to expect.  I understand that Germans find it relatively easy to navigate, while those of us from further away find it more challenging.  No surprise there – relocation is always smoothest when you have a local guide.

Thus, How you approach that transition and the resources available to you to help you adjust sets the tone of how you progress through the learning curve that follows.

Q. Isn’t there anything good about Denmark?  A. Sure.  I miss cheap cell phone plans, ubiquitous SCANPAN products and the fact that prices on the shelf include taxes.  I also think they have some great ideas about design and ergonomics (half of my furniture was Danish before moving to Denmark) that would be good here.  I even enjoyed watching Australian shows that we don’t get in North America (ie. Masterchef Australia is a very good show!)  I wouldn’t move there for those items.

Q. But you’ve acknowledged your social skill suck.  A. Actually, What I was really referring to is just that I’m more of an introvert, but living in Denmark really compounded the problem.  In hind sight, there are steps you go through when adapting to a new culture.  See wikipedia’s culture shock page.  Perhaps I didn’t give it long enough, but I can recognize that the honeymoon phase ended within days, and the negotiation phase never really stopped.  As soon as I felt like I was getting the hang of things, something else would catch me off guard – and often was accompanied by a serious financial penalty.

You do lose your sense of self when you’re trying to find your way in a new culture, and that can be pretty hard on an introvert when trying to find a new balance in a new country.

Q. But people tried to help, didn’t they? A.  Yes!  Some people helped tremendously, some people went really far out of their way to help, and some people were actually antagonising the situation (probably without realizing it).  And sometimes a person was in more than one category.  I have eternal gratitude to those who tried to help – and wish that I’d followed up on two offers to help that I didn’t, early on. (One from a complete stranger who found my blog, by the way, but lived over an hour away!)

I will also always be ready to jump to help the Dane who stepped in to help us get to the airport on our way out.  Truly, he went out of his way to help us out when things were darkest for us.  Alas, he’s since moved out of Denmark, citing some of the exact same reasons that were factors in our departure from Denmark.

Q. So what now? A. I’m done with this.  The lawyers will decide who’s at fault, eventually.  I can guess some of what was said about me in Denmark – and you know what, I just don’t care anymore.  When the whole story comes out, people will be free to make up their minds then.  In the meantime, I don’t care what you think you know – I want to get on with my life.  If you want to call me names based on what you think you know… well, that’s up to you.

Now, there’s science blogging to be done, code to be written and those in Denmark can decide to ignore me or not.  This is a blog – and you can always chose not to read it.

New Years Resolutions

I’d started writing this back in December, when new years resolutions were still reasonably in fashion.  At this point, I may as well just post it, and then do my best to hold myself accountable… welcome to February.

Fresh off of the worst year of my life, 2013 is starting to look like it might be shaping up in a good way.  From 2012, however, I’ve taken my lumps, so to speak, and wanted to convert that to lessons upon which I should work for next year.  Here goes:

  1. Every minute with my daughter is precious – keep it as a top priority. 
  2. It’s ok to get angry, and I will do it when it’s appropriate.  I can think of several examples of situations in which highly offensive things were said to me in Denmark and my reaction was to brush it off and keep a good face.  In hindsight, I think that just let people think they could walk over me, and I’m not willing to let that happen again.
  3. Let no detail go unplanned.   It may be obvious, but when someone says “don’t worry, we’ll figure it out later” they probably mean “you’ll pay for it later.”   Or, at the very least, they’ll try to make you pay for it later…
  4. Stop, think and then act.  Rarely do you need to act instantly, and knowing when you need to is an art, but most of the time you can pause to think things through before lurching into action.
  5. Learn more about the people around me.  After a year in Denmark, between the language barrier and tightly closed social networks, I’ve realized that my conversation skills have suffered greatly and that needs to be fixed.  It isn’t rude to pry gently into people’s lives.
  6. Be more welcoming of people new to the country. Clearly obvious.  I don’t want to do to others what the Danes to do visitors to their country.
  7. Work Harder.  Clearly this is just a throwaway, but I have goals that I want to achieve (academic and personal), and I want to hit them all.
  8. Do more exercise. I’m going to get back in to fencing and all the other stuff I couldn’t afford while in Denmark.  One should never neglect their health. (Yes, I did some running in Denmark, but only in the last few months before we left)

See, nothing outrageous or otherwise.  Just a few personal goals for the year.  How many will I keep, though, is a different story.