Updates – Oct 2011.

So, my thesis with the requested changes has gone back to my supervisor.  The process we have going is pretty…  unstructured.  At this point, I’m not sure what happens next.  In theory, it should now go to my committee, but who knows when that will happen. My external examiner isn’t scheduled to get it until mid december, which means my thesis defense can’t be scheduled until February at the earliest. Thus, I more or less have  4 months of thumb twiddling penciled in, unless my committee decides they want me to do another experiment. (And I’d probably have some choice words about that plan.)

So, with that said, I have a couple projects to “wrap up”, if you consider it wrapping up to be a) starting a project that won’t appear in my thesis, and b) doing some maintenance work on an open source project that my committee disregards because its not biology.  At worst, that’s about a week’s worth of programming (probably 10-15 hours, really), and getting things organized for someone in the lab.  (Hopefully a few emails I can take care of this afternoon.)

So, that has left me pretty focused on the post-thesis phase.  While I do have plans, I’m just waiting for an airplane ticket to be booked before I announce things. Until there’s an actual date, I’m not sure I feel comfortable spreading the news just yet, just in case everything suddenly crashes down and things don’t work out the way I expect them to.  All I can say, for the moment, is that I’m incredibly excited by the job description and the opportunity to work with the people I have already met, and of course, to meet everyone else there.

(I should mention that I was horribly jet lagged when I met them all the first time, but they all left a great impression, even if I’ve forgotten a few names…)

So, on to blogging, which is the next big thing that I’m mulling over.  First, I haven’t discussed blogging with my prospective employer, so I’m quite sure where things will go.  Of course, I don’t think it’s appropriate to blog about one’s workplace in any great detail, but some corporate bloggers have done a great job of it by discussing issues important to the work place.  In any case, I can see myself doing a few things:

  1. Continuing along the same path, and blogging about next gen sequencing – with a slightly more corporate bent. (which is a hint about what I’ll be doing next.)  There will be plenty of NGS related topics that I’ll be watching, and I’m certain to have an opinion on many of them.  (Who’da guessed?)
  2. Continuing along the same path, but diversifying to other topics in science so as not to focus on science tangential to my work.
  3. Adding on new topics about moving to new lands (is that a hint?).
  4. Adding on new topics about things more personal to me. (photography, music, etc.)

yes, my version of foreshadowing is a bit heavy handed.

And, last but not least, the other two things on my mind:

I’m seriously considering releasing drafts of my thesis on the web.  Now that my supervisor has agreed that my biology project is not likely to lead to a publication (and yes, that was the bulk of my work for the past year), it’s unlikely to meet much resistance.  I won’t do it until I get a go-ahead from those affected by the work, but it’s a project I’m working on, as I’d love to get more feedback.

And, finally, I had plans to write out summaries of some of the papers I’ve read on my way to wrapping up my thesis.  I haven’t decided if I’ll do this yet, but it would probably be a great way to help study for my defense.

In any case, that’s what’s on my mind this afternoon. And now that I’ve gotten it all down, I can clear my mind and get back to some of the other things I’ve been neglecting this past week.  Whee… errands!

Are we there yet?

I haven’t posted in a while – mostly I’ve just been tying off loose ends and endlessly reviewing my thesis while I wait for comments.  Alas, the 2 weeks has turned into 4, and scope creep is affecting things, but I think it’s finally under control…  at least, that’s what I keep saying.  If a batch of samples hadn’t been mislabeled by someone in the lab, I probably would have had those loose ends wrapped up today. &@$#ing lab mishaps!

Moving along, I’ve also had the chance to reflect a bit on my journey through grad school, and I thought I’d share a little graph I’d prepared:  How much time I thought I had left at each point of the journey.

You’ll notice several features are prominent.  One is the naive expectation that I could be done in under 4 years.  That lasted for a while, but it started shallowing out… and then the feeling of depression and hopelessness hit, at which you feel you’re never going to get out.  Once that passed, I thought I’d be done soon, but that has now dragged on for 9 months and it seems like it might just drag on a bit longer.  I’d debated adding a second spike, as last week I seriously considered just walking away when the latest “one last thing” wasn’t working out…

Anyhow, you can also see I’m extrapolating a bit past the five year mark, which I’ll have reached in january 2012.

Several lessons can be learned from this:

  1. Timelines mean f@%k-all, because it is not in anyone’s interest except your own to graduate. (Cheap trained labour is hard to find and if you don’t push, no one else has a reason to push for you to get out.)
  2. Your project will have snags.  Lots of them.  See point #1.
  3. You will encounter frustration and depression.  I’m glad it only hit me once – and yes, you can work through it. For me, it hit when I realized I had no hope of meeting my original timeline – see point #1.
  4. Getting out is also not nearly as smooth as you might think… there’s still no one except you who has an interest in seeing you get out quickly – and your university probably won’t go out of their way to help. See point #1
  5. There will always be “one more experiment” or “one more validation” to do. You will have to draw a line somewhere, otherwise, see point #1.

I’m sure there are plenty of other lessons as well, which I’ll undoubtedly be writing about in future posts, but those are the first few that come to mind this evening.

EDIT: I should probably mention that there have been many people who have helped me, so the above should be a reflection of the institutional lack of interest in your graduation, not of any one particular person.

Recap for August 2011

So I’m back.  Finally.

About 4 weeks ago, I cut off all of my “time wasting” interests for the sake of completing my thesis and then went all out in writing the damned thing.  As it happens, it was a great way to work.  No twitter, no blogging… no distractions.  I simply sat and wrote for 6-8 hours a day for 3 weeks and two days and banged out a version of my thesis to hand to my supervisor.  Given that I’d already written about 80 pages before pulling the internet plug, that was roughly the equivalent of 100 pages in ~15 days. I’m not unhappy with that.

But, of course, life doesn’t stop while you’re working on your thesis.  I’ve had to do a number of other small projects in the meantime, and a few big projects as well.  The biggest is that I have figured out where I’ll be going after I defend my thesis.  The open question is when that will be, as I still don’t have a defense date, but I am going to push for it to happen as quickly as possible.  For now, I’m going to keep the specifics quiet, but I’ll let everyone know in a few days.

Otherwise, I do know that my wife and I will be moving out of Vancouver, so we’ve begun the process of winnowing down our possessions.  I’ve given away a few potted plants, sold a lot of stuff on craigslist, emptied out drawers, recycled a ton of paper and even had a (very poorly attended) garage sale.  The fun never ends!

More noticeably to the internet, I’ve also switched internet service providers.  Despite the fact that we’re moving, our previous provider was unwilling to extend our current contract, and instead wanted $50 a month more for the same level of service, which just annoyed me – so I made the call to their competition.  Unfortunately, I didn’t realize that the new ISP actively blocks port 80, which took down my website. By pure fluke, I already had a hosting plan that I had been planning on canceling and they had recently started offering wordpress blogs – So, what you’re now seeing is no longer hosted from the computer in my living room. A big thank you to the staff at namespro.ca who helped make the transition reasonably seamless – other than having to wait over the long weekend for the right staff to come back to work to migrate my account. (=

Of course, the other internet change is that my email is no longer hosted from my home computer anymore – but that’s another long story. (However, the experience of running your own email server is pretty awesome – I highly recommend it if you have the opportunity.)  More to the point: If you tried to reach me over the past week and didn’t get a reply, that was the reason.  Sorry!

I also discovered that 4 weeks of isolation is great for reminding you of all of the blog topics that you should write about.  I have a couple more days of web site migrations to do (such as re-uploading the missing pictures from the blog, moving a few other hosted pages to the web server, etc), but once those are completed, I’ll be back on the blogging band wagon – and I have lots of ideas to write about.

In any case, thanks to everyone for their patience during my disappearance – and thank you for everyone who supported me while I was hunkered down and busy writing.


I went to a seminar on thesis writing last year.  They warned us that this would happen…

There’s only so much time in a day.

I feel guilty if I’m not working on my thesis.

I feel guilty if I’m neglecting my blog.

I feel guilty if I’m not working on other projects.

I feel guilty if I work instead of spending time with my family.

Given the finite amount of time available in a day, it’s a fine balancing act.  I just hope I don’t drop something…

10 Tips for how to get the most from your PhD.

I’m clearly late to this conversation, but because I disagree with the first two contributors, I figured I might as well have my say.

First, there was @Katie_PhD‘s post on “How to make the most of your PhD: The road less traveled“., which (alas) doesn’t give you much of a sense of how to get more out of your PhD.  It’s a great piece, so don’t get me wrong – I’ve read it several times already – but there aren’t any tips for graduate students.

Following on, Nick at “For Love of Sciences” wrote a list of tips that could help incoming and early PhD students get more out of their PhD.  Unfortunately, I’m not sure I really believe Nick’s points cover the topic the way I’d like to see it covered.  Some of them are dead on: Yes, you should move out to a new city, to find a new environment and challenge yourself, but other’s I find myself disagreeing with Nick.  Alas, that’s the point of graduate school, really – to stand up for what you believe in, and boldly state when you think other people aren’t nailing the point as accurately as possible.

So, without further ado, let me introduce my top 10 tips for how to get the most out of your grad school experience.

1. Say yes, until you learn to say no.

When you start graduate school, you won’t know enough about which avenues are the right ones to follow up.  Learn to say yes at first, to tackle any project that comes your way.  You’ll find yourself tackling good projects and bad projects and, as time goes by, you’ll learn how to tell which projects are the bad ones in order to start saying no to them.  When you’re ready to graduate, you’ll even have to turn down a few of the good ones in order to keep your PhD from dragging on too long.  So start with yes, but learn how (and when) to say no.

2. Learn to communicate.

Half of the challenge of a PhD program is to become a good communicator.  Define what good communication means to you and then bust your ass to figure out how you can become as good as possible at it.  Whether that’s communicating science to non-scientists, communicating with your peers, blogging, twittering or even writing grants, make a commitment to learn to communicate in every possible form and then to get better at it.  At the end of your PhD you are going to be judged by how well you can defend your ideas, so why not practice it as often as you can?

2b.  Learn to teach.

Teaching is just another form of communication, but it’s an important one that just can’t be overstated.  If you become an academic, you’ll be evaluated on how well you teach your students.  If you become a blogger, you’ll be evaluated on how well you can teach your audience.  If you become an entrepreneur, you’ll be evaluated on how well you can teach your board about your technology.  The job of a scientist is always teaching and communicating, so get as much practice (and hence feedback) as you can while you can.

3. Take advantage of your university’s resources.

Every university that I’ve had the pleasure of visiting has had some form of courses for it’s graduate students to learn new skills – TAKE THEM!  I’ve gone to some really cheese-tastic courses, and I’ve gone to some life-altering good ones.  You never know which one is which till you try them out, but if you don’t try any of them, you’re tossing away a perfectly good opportunity.

4.  Meet your future life partner.

I cheated on this one – I met my wife while we were doing our masters degrees together, but it was still graduate school and I had been planning on doing a PhD at the time.  Regardless, when else will you be surrounded by people who are fascinated by the same things you are, smarter than you are, and are fantastically interesting people in their own right?

4b.  Make some great friends.

Yeah, even if you don’t meet the love of your life, you can definitely find a few friends.  I’ll admit, I haven’t made a lot of close friends during my PhD, but I’ve made up for that with a wide net of professional contacts and having had the opportunity to rub shoulders with a lot of fantastically interesting and successful scientists.  I wouldn’t have traded it for anything.

5. Decide what you stand for, and stand for it.

Along the long and winding road of your PhD, you’ll discover situations that test your morals, your sense of dignity and your ideals.  Everyone is sorely tempted to sweep a bit of dirt under the figurative carpet of their project in the name of having results to show off.  If you don’t believe me, spend some time reading the retraction watch blog. What separates the good scientists from the bad scientists is the moral code to which they hold themselves.

I’ve taken stands on open source code, on re-doing experiments and on re-coding units that were just “good enough.”  Grad school gives you a great opportunity to do the things that matter to you – and do them well.  This is one of the few times that you get to show people who you really are and not compromise on it.

6. Keep good notes

Pretty much everything you do, you’ll either have to show someone else how to do it, or do it over again later.  The better your notes are, the easier things will go for you – and that includes when it comes time for you to write up your thesis.  Trust me, good notes and documentation will make your life SO much better when you’re writing a chapter and want to figure out exactly how that algorithm worked, or need to make last minute changes to a poster  at 3am and can’t remember how you churned out that table…

7.  Be a sponge.

Grad school is also one of the few times that you can really delve into projects that you wouldn’t otherwise have a chance to pursue in a corporate environment.  I’ve learned such random/wonderful things as how to play ping pong, how to use professional publishing software and how to draw cartoons.  You never know when these things will come in handy.   (For the record, there are far better examples, but those were way more amusing to me.)

8. Face the challenges.

Not many graduate students get slapped down for trying to take on more responsibility or to tackle the tougher projects.  I’m constantly amazed by the people who just quietly slide through grad school without leaving a ripple behind:  Life doesn’t start once you’re finished – it’s already going on, so hiding behind your desk isn’t going to help you get anywhere.

Perhaps I’d sum it up this way: Have the courage to face problems head on, tackle projects that are bigger than you are and throw yourself into the fray.  The worst thing that’s likely to happen is a bruised ego, but even that’s sometimes a lesson worth learning – and it’s a lesson that’s much easier to learn as a student than in the corporate world.

9.  Don’t give up.

People will ridicule you, people will flame you in emails, projects will misfire, scholarship applications will be rejected.  These are facts of life.  You can’t make everyone happy all the time and even keeping yourself happy can be a challenge some days.  Remember that there is always a light at the end of the tunnel and if you persevere, you will get through.

An investor once told me a brilliant piece of advice in relationship to startup companies, which I’ll paraphrase and apply to grad school.

“Grad school is like a roller coaster: some days will be crazy high, some days will be desperately low.  Sure, you can enjoy the highs, and you’ll despair in the lows, but don’t let either of them change your course – keep a straight and level path and you’ll get through to the end of the ride. “

And that brings me to the last point…

10.  Enjoy the ride.

The longer you spend as a grad student, the more impatient you’ll be to leave, but that doesn’t mean you can’t enjoy the time you spend there.  You’ll rarely have such a wonderful combination of responsibility  (or lack thereof), freedom (or at least, lax deadlines) and community (how ever you want to define it.) –  Remember to appreciate what you have while you have it, because things will change once you hand in your thesis.

Here’s to that day coming as soon as possible!  Cheers!

External examiner required

It’s one of those long standing traditions of academia – having your work examined by someone who has no stake in your future career.  In theory, this should liberate the external examiner from feeling obliged to grant unworthy applicants a degree, but in practice, I have the sinking suspicion that, to the examiner, it probably just feels like one of those thankless tasks that really doesn’t have any reward.

Although I can’t actually do anything to make it more rewarding for whomever steps up to the plate for my thesis, other than try to make my writing as easy to read as possible, I thought I might start by casting the net a bit wider than the average grad student’s search – in the hopes of finding someone with a real interest in reading my thesis.

If this were a job application it would go something like:

Wanted: One External Examiner.  Must be an academic with interest in at least two of:

  • Chip-Seq Algorithms
  • Large databases
  • Human cancer variation
  • Breast cancer

Applicant will be required to read and comment on a 120+ page document, and either appear at an as yet unscheduled thesis defense, or to send comments via email.  Successful applicants will be allowed to twitter or blog the defense, if desired.. Compensation will not be commiserate with experience… or with anything else, for that matter.

Does that appeal to anyone?

In any case, I fully expect to start putting together a list of names in the next couple weeks.  I should mention I’m not really expecting anyone to step forward, but I would be thrilled if someone did.

Other Thesis Related Matters: The document currently sits at 92 pages of text/figures/refs, with what feels like about 65-70% of the content I want to put in.  I anticipate having a reasonable first draft in about 3 weeks, putting my thesis defense roughly in November-December.  I’m still debating doing all of edits in an open manner on the web, but I will not be opening up any of it until after my committee has seen at least one draft, at the earliest.

What is the purpose of a Post-doc?

No one has ever sat down with me and explained the various purposes of each degree. I’ve figured out what Bachelors and masters degrees are good for (basic training, specialized training respectively) and the purpose of a PhD was spelled out to me when I was in industry (showing you can take responsibility for your own research).  However, no one has ever explained to me why I should want to do a post doc.

As far as I can tell, the best excuse for a post-doc is to learn a skill that you missed during your PhD, or, failing that, if you didn’t get enough publications during your PhD, you can pump out a few more here.

But, why would anyone feel the need to spend another year or two…. or five (or ten!) doing a post doc to learn a set of skills?  I just don’t see that being a great reason.

I’ve also heard that post-docs are often done to get into a good lab, so that one can add to your network of connections, or perhaps to put a good PI’s name on your resume.

I’m not sure I buy either of those, however.  In this day and age, one can make connections through many other methods.  Working for someone isn’t the only way to develop a network.  And really, I would like to think that your future career is decided on more than just having a good PI’s name on your resume.  Finally, the better the PI, the less likely they are to have the time to invest in one of their post-docs.

Last time I checked, Post-docs aren’t even treated like staff at universities, they don’t get benefits, they don’t get paid like the highly trained researchers they are, and they don’t get an actual degree out of it.

So… why do we have post-docs?  And why should I consider doing one?  As a keystone of the academic world, it might have some merit, but is that the only reason why someone should consider it?

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.


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.