It’s done!!!

Ok, It’s now official:  I’m only a few more hoops away from my PhD being complete!

My defense was incredibly smooth – My committee was incredibly friendly and kind, and I can finally look at closing the door on the last 5 years of my life.  Pretty soon, I’ll be Dr. Fejes.  Not really sure what that changes, but I had thought the day would never come.

What a long journey it’s been, tho… and so many twists and turns.  I put up a slide at the end to thank the people who’ve helped me get through it all, but I really couldn’t list everyone… and I realized I missed the most important people of all: my wife and family, who’ve watched the whole process unfold.  Really, their support has been everything to me, and I wish they could have been here for the defense.

Now, if you’ll excuse me, I think I should lie down for a bit.  Jetlag and oral defenses should really be counter indicated.

By the way, I think this is the last time I’ll be able to use the “Grad School” category for a post.  Good riddance!

Day of Reckonning

I’m standing in my hotel room, pacing around while I practice my defense talk.  The currently length is 18:36, which is just under the maximum 20 minutes.  I hope, if I have any neighbors in the next room over, that they’ve brought earplugs.

Frankly, I’m pretty nervous about the exam.  I have no idea how it will go.  What I know, I know well.  What I don’t know, I know that I don’t know at all.  I just hope my examination committee can accept where those limits are.

Anyhow, 12:30pm is about 14 hours from now.  I plan to spend at least 6 of those hours sleeping, an hour traveling to campus, and a few minutes, at least, picking up sandwiches.

Considering that it is currently 7am in Denmark, and I still haven’t adjusted to Vancouver time, I’m amazed that I have any functioning brain cells left at all.

On that note, I’m going to run through it again.  On your mark, get set, go….

“Nominated to receive a Ph.D degree”

Three weeks from my defense, and I get this email:

WISH to DOUBLE YOUR INCOMES? In this business that allows you to receive
your knowledge and Our wide experience that you want! Bachelors, Masters
and Doctorate degrees of various specializations are already waiting for
you! They are fully verifiable! Many people share the same frustration,
they are doing the work of the person that has the degree and the person
that has the degree is getting all the money. 

We accept your phone calls 24 hours a day, not to postpone your 
Improvement of qualification.We send the certificate to all countries

Who knew, I could have had the PhD without doing any of the work – and I’d double my income because I’ve been doing the job of someone with a PhD…

Drat – seriously, people, where were you 5 years ago?  And hey, they even ship to Denmark!

Committee Set

Just a quick follow up post.   I’ve heard from the university today about who the chair for my exam will be, and I couldn’t be happier.  Oddly enough, I’m starting to look forward to the exam.  I know most of the examiners, and they’re all tough, but fair.   I can’t wait!

Thesis Defense… scheduled!

So, it looks like I will have a shot at getting my PhD after all – the first PhD in my family, really, despite being surrounded by innumerable relatives with Masters degrees.  Anyhow, as I was recently notified in an email:

Your Final Doctoral Oral Examination has been scheduled to take place on Friday, March 30, 2012 at 12:30 PM in Room 200 of the Graduate Student Centre (6371 Crescent Road).

Anyone who feels like attending will be welcome, of course..  I have no idea how large the room is, and if you arrive late, you won’t be allowed in, as per UBC regulations.  As far as I’m concerned, it’s also bloggable and tweetable – though I’ll be a bit too busy to do it myself. (-;

I have to admit, the scheduling was a pretty tight squeeze – and a huge thanks goes to my supervisor’s administrative assistant for helping arrange it. Without her help, I wouldn’t have been able to defend till sometime next year. No names mentioned here, of course, but I will be proposing naming my daughter after her.

I’ll also be thanking CLCbio for their help as well, but it’s a bit premature for that.  And,  I don’t think the Danish government name registration agency would allow me to name a child after them anyhow.

(As a closing remark, my long standing self imposed condition was that I had  to get the thesis done before Robert Jordan’s (and now Brandon Sanderson’s) The Wheel of Time series was completed…  the final book of which is now due to hit the stores January 2013.  For a series of books I started reading 20 years ago, I have to admit, I’m cutting it a LOT closer than I expected.)



It’s late, and I don’t want to stay up to write a long post. I have stuff planned, but I’ve been busy lately.  I just wanted to share the news that my thesis passed my committee’s review, and after several hours of LaTeX work, it has now passed the university’s checks as well.

In theory, I should just be able to drop off a copy in person, but I have a feeling that its going to be a bit more challenging than that from Denmark.

Progress is progress.  I’m celebrating with a late night bowl of musli.   (:

Preparing for “the After”

I’ve been thinking quite a bit about “the after”. That is, the post-PhD period. Personally, I’ve got a job lined up and the details are generally falling into place. While I’ll save the talk about moving for later, I thought it would still be a good opportunity for reflection, as things could have turned out quite differently.  I searched for other posts on the topic, but mostly found advice on how to become an academic, or how to find industry jobs – not quite the same thing as how to gracefully exit a PhD.  (Of course, it could be argued that I’m not exactly exiting gracefully and shouldn’t be giving advice, but that’s a matter of opinion.)

Several things stood out for me in the process. Right from the start, I probably shouldn’t have started thinking about “the after” until closer to my defense. This was a major mistake on my part.  Without a defense date in hand, I was simply operating on someone else’s assurances that I’d be done at a given time. Regardless of who it was that said it was possible, dates WILL slip until a defense date has been filed with the university.  As a grad student, you are dependent on other people setting aside time to edit, comment and process your thesis.  Your tuition does not pay their salaries.  Well, actually, it does, but they’re still not a service industry.  (ie, if your university gives someone 6 weeks to respond to your thesis, they’ll take 5.999999 weeks, if not 7 weeks.)

Anyhow, given that I messed that part up, there were other valuable lessons that I learned.

First, take the time to work out what you want to be doing “after”.  There’s no point in hunting for your dream job, if you don’t know what that dream job is.  Easier said than done, but an important first step – and gets my longest rant.  (feel free to skip down, if you want the tl;dr version)

Personally, I had spent a lot of time on this one issue, but even so, I wasn’t really sure what I wanted. One of my committee members took the time to promote the academic career to me about a year ago, and it left an impression on me.  I had to re-evaluate if that was something that would fit – and for nearly a year I seriously contemplated an academic track. A more ruthless consideration of whether I was happy with the actual job would probably have helped.  (Readers of my blog might remember a few posts when I was seriously debating the two possible courses.  In the end, I came to the conclusion that i just can’t see myself pursuing grants… but I would be happy to talk with investors again.)

In fact, I even went so far as to visit a highly respected academic institution who’s researchers work in the field in which I was most interested only to discover that I just didn’t fit there.  It wasn’t something I knew before going, but it became incredibly apparent after visiting.  While there, I gathered a lot of information that I needed in order to do some serious soul searching to figure it out. To have saved everyone the time and effort, I should have spoken to more people before – and filtered some of that advice much more rigorously.

I also had an opportunity to do something that would have given me a lot of responsibility, to work with a great team (ok, it was really an exceptional team) and to stay in Vancouver – and in the end, I had to turn it down for the simple reason that I really wanted to stay “hands on” in bioinformatics a little longer.  Once I figured out what it was I wanted to be doing, the choice became clear – even though the decision was still hard to make.  (I might kick myself for it later, but that remains to be seen.)

Second, while I don’t think you should be working on your “after” plans from the start of your graduate degree, remember that networking starts long before you’re ready to graduate.  As it turns out, I met the contact that led to my position several years ago, well before I was even close to finishing.

Actually, that itself is probably worthy of it’s own post.  However, the short version of how I found my “after” plan involves meeting and talking with someone over several years at AGBT, where I would spend 12 hours a day taking notes, 6 hours trying to network at parties, and maybe 5 hours sleeping, all while jetlagged.  The last time I met him in person I was working through a 9 hour jetlag.  The fact that I was able to hold coherent conversations at all, and that the people I met didn’t write me off because of it should be considered a miracle! You never know who will lead to a great position – or who might point you in the right direction – and there’s no reason to think that only contacts you meet at the end will be the ones that can help you find your dream job.

There are two minor points that should be apparent from my example: 1. even when you’re not at your best, try to be at your best!  You never know who will lead you to a job, a contact or a collaboration.  Networking is important, and I can’t stress that enough – even for a nerd like myself – even when you don’t think you’re networking.  2) Keep an open mind – but don’t waste other people’s time. I’ve interviewed people for positions before who had no real interest in taking it, once it was offered.  It doesn’t help anyone out, and doesn’t reflect well on you either.

Third, set a time line.  This may be the one thing I did right – Once I had an offer, I set a time limit on when I wanted to make a final decision. This had several effects:  It made me invest the time that went into the search up front, it also forced me to stop looking at some point and, of course, it leveled the playing field, so to speak – everyone I spoke to knew when I expected to have a decision so that the process wouldn’t be dragged out.  Admittedly, it felt dragged out, but that’s probably the time dilation that comes from working on a thesis.

A few things could have gone more smoothly, however: I should have had a time line that matched up with my defense date, rather than with my anticipated time of completion.  However badly off the time line was, it forced the process to be relatively transparent both for my self and for the people I spoke with.  I certainly didn’t want to leave anyone waiting for an answer.

The time line also had the effect of clearing off my desk.  Once the process was done, at least I could focus back on the task at hand: finishing my thesis.

Fourth, use your time wisely.  That might sound like a silly warning, but I could have done better.  There will come a time during your thesis writing when you realize you have nothing to do. You’ll be waiting on people to get back to you, or waiting on revisions, or something of the sort.  It is a great time to start your job search.

Having jumped the gun on this one, I’m instead using the time to plan an inter-continental move, so I guess I’m not doing too badly.  Yet, it did make the writing period a bit more stressful as I was setting aside time to meet/phone people while trying to hash out the drafts and chapters.  Deciding your career path does have a strange tendency to distract you from writing about your work.

Also, and as a complete aside, airplanes and laptops are a great combination.  You can write an awful lot without any distractions when you have a total of ~1.5 cubic meters of space – and no where to go.

Finally, talk to everyone you can.  If you’re not dead set on one specific job, it can really help to have sounding boards with whom you can discuss your options.  The more you know about things, the better.  Of course, that’s not to say that you should let people convince you not to do something you’d like to – but the more you know, the better prepared you will be for deciding where you want your life to do.

And, the corollary is, naturally, to listen to what they have to say.

So – recap time:

  • Work out your schedule so you know when you’ll be available to start the “after” part of your life.
  • Try to figure out what it is you want to be doing and get a clear picture of what you want and need.
  • Talk to people about what’s available that matches your dream job – or find out if your mental picture is real.
  • Build a realistic time line that includes deadlines for when you’ll have decisions.
  • Manage your time wisely
  • Talk with your friends to find out what they know – and to work through the tough choices.

If you manage to do all of that, you should be in good shape.

The next question, however, is: did I miss anything? What other advice should you give for planning your exit from your grad school degree?

How to be a successful graduate student

I have a weird perspective on what success is, I think.  To me, success is defined as achieving one’s goals, learning valuable lessons along the way and possibly making a significant contribution along the way.  I don’t think many people would argue with that – however, in academia – at least for grad students, success isn’t necessary measured with the same metrics. Instead, it seems to be measured by how many scholarships you get and how many first author papers you publish.  (Fair criteria, if you are looking for future professors.)

Looking around at the graduate students (and ex-graduate students) that I know (or knew) is an interesting opportunity for reflection.  I can ask the questions: Who did well and what did they do to achieve their success?

Just to be clear – I’m not specifically discussing my own lab!   (In fact, “labs” don’t really even exist where I am, so I’m just describing what I’ve seen over the course of all my years as a grad student here and elsewhere!)

First, I think it’s pretty clear that there’s a relationship between time spent with advisors and the success of the student.  This isn’t necessarily an obvious correlation, but it appears to be true.  From my perspective, a PI’s time comes with a lot of benefits:

  • More opportunity to learn from those who already know something about a field.
  • More input into your project from those who have made the mistakes and can guide you to success.
  • Access to more “hot topic” projects that will get you more publications.

These seem pretty self-evident to me.  The more brains you have on a project, the faster you get results, and the more results you have, the more invested your PI will be on your project.  (This is basically a self-reinforcing problem, where one student gets to be the “golden boy” and get all the guidance, and all the others do the work blindly and thus make slower progress… but I’m getting ahead of my self here.)

Second, a students’ ability to drop a project is a huge determining factor in their success.  Those students around me who are able to move from project to project quickly are the ones that get the most papers and opportunities.

Someone I’ve been working with has been forced to analyze and reanalyze the same set of data over and over for YEARS to get it just right.  His data is now old and stale, but he’s just not been allowed to move on.  While I understand that the data probably cost a huge amount, it would likely take all of $6,000 and 3 weeks to generate an infinitely better data set for him – but as long as he’s trapped on that data set, he’ll never be able to progress any further than the limitations of the original data.  Moving on would be the right thing, but he’s just not been allowed to do it.

Meanwhile, those graduate students I know that hop from item to item are always able to make the biggest splash. They spend three months on each project, and crank out four papers a year. TADA.  Instant golden boy material!

My own solution to the problem (of having a a dead weight project)was the wrong one, having tried to pull in side projects to gain success in areas where my main project was holding me back.  While all of my successes did come from those side projects, it led me head first into the next item.

Be clear on what success means. Despite my gains on side projects, I naively thought that getting software into production pipelines was a good thing.  Yes, I learned much from the process, but in hindsight, it was a disaster.

For bioinformatics software, producing an implementation of an algorithm that works is sufficient for getting you a paper.  Everything you do after that is a waste of time.  I invested hours into support, development and meetings that slowed down my graduation time by months if not years – and not one thing I did after the paper came out counts as a “success” in grad school terms.  Those projects were certainly successful for other reasons and there was good justification for doing the work I did, but those were all “fringe benefits” if you’re looking at my core “success” of grad school.  That is to say, no extra publications, no extra scholarships and no real credit where it was needed.

In fact, one graduate student I know wrote some excellent proof-of-concept code for his own project, which everyone realized was a great improvement over the current pipeline.  He was asked to help generalize the code for broader use, and his answer was a resounding “NO”. That’s a pretty gutsy move, but he’s also the one grad student I know with a huge track record of success. Draw what conclusions you like, that student did not get saddled with supporting, maintaining or coding for anything but his own projects – and that makes all the difference, seeing as he has a pretty awesome publication record to show for it.

Third, the resources available to a student determine what a student can achieve.  Again, probably self-evident.

One of my brilliant colleagues has been required to write grants, scrounge for money and spend time looking for sample donors to move forward on their project. I think this is a great learning experience for someone who wants to be an academic, but it does tend to suck away time from other key ingredients – like analyzing data and publishing it.

This also applies to students who lack good lab equipment and access to important reagents.  I knew people in labs that were so poor, they’d spend days doing things “the hard way” when richer labs would simply walk out and buy a kit.  (Yes, kits are expensive, but they work.)  All of these little things add up and can contribute to your success or failure.

Resources also play a part in your ability to network.  Going to conferences does a lot of good for you in so many ways.  You learn about new things, you see other people’s methods (realizing how yours probably don’t stack up), you meet new people (including some very important and interesting people) and you get challenged to elevate your game.  The only problem is that doing this requires more money.  If you don’t have money to do your research, you probably don’t have the money to travel either.

Fortunately, networking can also be done for cheap, such as blogs and twitter – and not to forget the good old standby email and phone techniques.  You may have to go out of the way to make them happen, but you can do it if you invest your (limited) time wisely.  I really don’t think I need to emphasize the value of networking, which would be it’s own post, anyhow, but you can alway tell me if you want to hear me ramble on that topic.

Alright – let me wrap up this topic, then. To be successful, you need:

  • Time with your PI
  • Ability to move on when things aren’t working
  • Resources to do your work and to establish a network

Got it?  Great!

Fortunately, there exists a cure for the resource problem: scholarships!  Your job as a grad student is to get yourself a good source of money to support yourself, thus freeing up resources for your lab while simultaneously enabling yourself to network and travel further to meet new people, who can help you find new and interesting projects and collaborations that will help you get more publications, which will give you more “face-time” with your PI because he’s interested in all these projects…

Did you see that coming?

And suddenly, you’re back to the chicken and the egg problem:  Having more face time with your PI gets you more success, and more success gets you more face time with your PI.

So, I suppose the lesson here is: Find a PI that will invest time, money and effort into your projects, and one who is willing to help you succeed and progress in your project – and is happy to move to new projects when the one you’re working on doesn’t work.

And if you can follow that recipe, you will be set – or, you’ll already be the golden boy and that recipe will follow you.  Either way, happy grad schooling!

Letting the Cat out of the Bag.

It is finally official – I’ll be leaving Canada and going to Europe (Denmark) in December – joining the team at CLC bio in just over a month. You’ll have to excuse my holding off on letting everyone know.  Of course, things have been in the works for some time yet, but the last few pieces have only clicked into place this week.  And, of course, one doesn’t want to jump the gun by announcing these things before everything is in place.

Of course, this doesn’t mean I’ve finished my PhD yet.  There are a still a few more hurdles – my thesis has to go through my committee and the external examiner, and I still need to officially defend it – but it was looking like the soonest that could happen would be February, and with everything going on, my wife and I decided it would be better to just start the process of settling in to Denmark as soon as possible.

So, consequently, if you read my blog, you’ll probably hear a little bit more about some topics that are currently on my mind: learning Danish (lære Dansk), traveling, maybe some cultural collisions (Danish people don’t have closets?)  and possibly some photography, depending on how busy I am.  (Yes, now that I’m not actively writing my thesis for 6-8 hours a day, I seem to have more time.)

But don’t worry – in the next month, I still have a few things I want to blog about, and likely a few papers to review.  Even though I’m leaving Grad School, I’m not leaving science behind.

To be candid, I’m looking forward to starting up at CLC partly because of the job, which already sounds pretty awesome, and because of the people.  I’ve met some of the people I’ll be working with – albeit briefly – and I’m excited to have the chance to work with them.  I can honestly say that they one one of the nicest groups of people I’ve ever met.  Must be something in the water. (-;

Anyhow, to complete the circular nature of this post (like all good fugues, which is the way to write a good post, particularly if you’ve read Gödel, Escher Bach, if that’s not getting way to involved) I have one last point to clarify. As foreshadowed lightly by the title of this post, yes, my pets will be coming with me – and undoubtedly my cat will be thrilled to be let out of the bag once we’ve arrived in Denmark… so the moving process will be bookended, effectively, by letting cats (figurative and literal) out of their respective bags.

Ollie - My wife says we have the same nose.

How to write a PhD thesis

After finishing yet another draft of my thesis, I thought I’d share some of the hard won pro-tips I’ve worked out along the way.  This, being my fourth thesis (one for each of my degrees, including my undergrads), was probably the best of the bunch. Let me tell you, by the time you’re on your fourth thesis, you’ve learned a few things.  So here they are:

Pick your Technology: The first step is to decide what software you’re going to use to write your thesis.  The minute you start, you’re going to be locked in with no hope of switching.  There really isn’t a way to transfer your work from one technology to the next, so pick wisely.  In the past, I’ve used Microsoft products, and I found them to be a very wasteful way to proceed.  This round, I picked LaTeX/Kile, and despite the 3-day intense learning curve at the front, things have gone very smoothly since. (Yes, only a programmer will appreciate the beauty of compiling a document – it’s not for everyone.)

Whatever you do, make sure you understand the ramifications of writing a 100+ page document in whatever software you chose.  A 10 page document in Word is nothing at all like a 100 page document in Word. (Hint: I found scaling with Word to be painful, particularly when illustrations are involved.)

Pick your Referencing System: Similar to the point above, in your thesis, references are your lifeblood – pick a system that works and start using it early!  Nothing says disorganization worse than trying to find “that paper” in a 50cm high stack.  The sooner you start organizing your papers, the better off you’ll be.

My trick was to use Texmed to get papers in the right format, then toss it into a .bib file with a quick annotation, so that I could figure out why I thought that paper was significant.  It cut down a LOT of time when it came time to add citations.

Organization: Writing a thesis isn’t hard, surprisingly.  The biggest, hardest part is organizing it.  My best trick was simply to write out alll of the headers, then write out in point form what I thought went into each section, then – one by one – expand the points into paragraphs.  Throwing in illustrations and references at that stage was a great help for writing as well – this helps you build the text around the information you have already gathered.

Once you have manageable small chunks to write, it was always easier to tackle them – and you never stress about having giant blank sections in front of you.

Communication & Feedback: Well, this is more of a wish list for my own thesis, but it would have made progress go quicker.  Once I had my outline of headings, I asked my supervisor to let me know if the topics I had included and left out were appropriate.  Keeping that loop tight can save time – particularly with the comments that said: “Please discuss topic X.”

Working with those who can provide you feedback is always a good idea – and the earlier you get it in the process, the easier it is to fix or prevent problems.

Keep track of your Progress: I found it very useful to keep a list of tasks (aka, sections) that I needed to write, and every time I finished a section, I could check it off the list.  Every time I did a revision, I’d write down a list of changes and then plow through that list, checking completed items off one at a time.  Not only is it better for making sure you aren’t missing things, it’s also easier to track your progress – which is the lifeblood of any major undertaking.

It becomes much easier to tell when you’re falling behind and need to pick up the pace, and it allows you to figure out what works best for you.

Set Goals and hold yourself Accountable: Yes, that may sound like fluff, but it made all the difference for me.  A colleague of mine is also working towards his thesis, and we came up with a great system where we meet once a week to share our accomplishments, and to admit our failures.  For added motivation, failing to accomplish your weeks goals got you a mark on the “beer list” – meaning you owe a beer to the other person.

Admittedly, owing a beer isn’t a huge motivation, but it does remind you of the consequence of not achieving your goals.  And missing your target too often will be a problem down the line, so this is a good way to make sure you’re staying on target.

I also have to say that in a project this big, there’s always the temptation to put off a goal for later because it’s just sliding by one day – and the final goal of the project is a long way away.  Don’t fall for it!  Those days add up, just like the beers.  Set your goals realistically, and then hold yourself to them!

Guilt management: This one always gets me.  When you have a project like this, it’s temping to think you need to work on it 24/7.  Realistically, that’s not going to happen, so figure out what schedule works for you.  My trick was to get up, spend 20 minutes reviewing my goals for the day – and then take a shower.  I do a lot of my best thinking in the shower, so it always helped me plan out what I wanted to write.  I’d then eat breakfast, while reading the days news… and then it was time to work.  On a good day, I’d work from 10:00 – 4:00 without much more than a few breaks.  Having put in a pretty solid 6 hours of writing, I’d go walk the dog and remind myself that that was a good day.  If I had goals to get done (see above), I’d return to it after dinner.

You are not expected to neglect your life to get your thesis done – but you are expected to focus on it during your prime working hours!  If you set aside a reasonable amount of time every day and meet your goals, that’s good enough.

Focus: That said, when you do set aside time to write, try to do it somewhere without distractions.  For me, a desk set in the corner of the room, facing a window that looks at nothing in particular was the trick.  Nothing outside to distract me, natural light to keep me awake and nothing around me to pull my attention away (except the cat) helped me get my focus and keep it for long periods of time.

Exercise: I can’t stress this one enough, really.  For me, getting out of the house a couple times a week for a good evening of fencing was really therapeutic.  When someone is swinging a sword at you, there’s just no room in your head for organizing chapters.  Setting aside my monday and thursday evenings to not think about thesis work, to get myself away from being sedentary in front of the desk, made a big difference. To paraphrase one of my favorite books (Microserfs), your body is not just a transportation unit for your brain!  Don’t forget to take care of it.

Cats: Do not let your cat write paragraphs for you!  Mine took a nap on the keyboard, and added 6 pages of “zzzzzzzzzzzzzzzzzz” to my thesis. Which leads me to:

Backups: Actually, since I was using LaTeX, I used revision control (SVN) to manage my documents.  Every hour or so, I’d check in my documents to make sure I had a copy.  I only ever used it once, but the one time I needed it, it was there – and it saved me several hours of trying to recreate something I’d lost.

Figures: Keep two copies – the original and the version you use in your thesis. And, keep them in the same place so you can always find it.  You will need to go back to the original many, many times, so having it handy – and separate from the one you’re using in the document can be a big help.

Remember you’re the Expert: The work you’re writing about is work you did.  No one knows it better than you do.  Write it out as if it’s a manual for someone who’s going to follow in your shoes… because someone probably will, and this is how they’ll continue on your legacy.

Enjoy it: Thesis writing is hard work, but so were the years you put in to get to this point.  Try to enjoy the process and make it as pleasant as possible for yourself – short of taking your laptop in to the bathtub, of course.

I’m sure there are other things, but that’s all that come to mind so far.  Feel free to add to the list in the comments.