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!

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.

>Nothing like reading to stimulate ideas

>Well, this week has been exciting. The house sale competed last night, with only a few hiccups. Both us and the seller of the house we were buying got low-ball offers during the week, which provided the real estate agents lots to talk about, but never really made an impact. We had a few sleepless nights waiting to find out of the seller would drop our offer and take the competing one that came in, but in the end it all worked out.

On the more science-related side, despite the fact I’m not doing any real work, I’ve learned a lot, and had the chance to talk about a lot of ideas.

There’s been a huge ongoing discussion about the qcal values, or calibrated base call scores that are appearing in Illumina runs these days. It’s my understanding that in some cases, these scores are calibrated by looking at the number of perfect alignments, 1-off alignments, and so on, and using the SNP rate to identify some sort of metric which can be applied to identify an expected rate of mismatched base calls. Now, that’s fine if you’re sequencing an organism that has a genome identical to, or nearly identical to the reference genome. When you’re working on cancer genomes, however, that approach may seriously bias your results for very obvious reasons. I’ve had this debate with three people this week, and I’m sure the conversation will continue on for a few more weeks.

In terms of studying for my comprehensive exam, I’m now done the first 12 chapters of the Weinberg “Biology of Genomes” textbook, and I seem to be retaining it fairly well. My girlfriend quizzed me on a few things last night, and I did reasonably well answering the questions. 6 more days, 4 more chapters to go.

The most interesting part of the studying was Thursday’s seminar day. In preparation for the Genome Sciences Centre’s bi-annual retreat, there was an all-day seminar series, in which many of the PIs spoke about their research. Incidentally, 3 of my committee members were speaking, so I figured it would be a good investment of my time to attend. (Co-incidentally, the 4th committee member was also speaking that day, but on campus, so I missed his talk.)

Indeed – having read so many chapters of the textbook on cancer biology, I was FAR better equipped to understand what I was hearing – and many of the research topics presented picked up exactly where the textbook left off. I also have a pretty good idea what questions they will be asking now: I can see where the questions during my committee meetings have come from; it’s never far from the research they’re most interested in. Finally, the big picture is coming together!

Anyhow, two specific things this week have stood out enough that I wanted to mention them here.

The first was the keynote speaker’s talk on Thursday. Dr. Morag Park spoke about the environment of tumours, and how it has a major impact on the prognosis of the cancer patient. One thing that wasn’t settled was why the environment is responding to the tumour at all. Is the reaction of the environment dictated by the tumour, making this just another element of the cancer biology, or does the environment have it’s own mechanism to detect growths, which is different in each person. This is definitely an area I hadn’t put much thought into until seeing Dr. Park speak. (She was a very good speaker, I might add.)

The second item was something that came out of the textbook. They have a single paragraph at the end of chapter 12, which was bothering me. After discussing cancer stem cells, DNA damage and repair, and the whole works (500 pages of cancer research into the book…), they mention progeria. In progeria, children age dramatically quickly, such that a 12-14 year old has roughly the appearance of an 80-90 year old. It’s a devastating disease. However, the textbook mentions it in the context of DNA damage, suggesting that the progression of this disease may be caused by general DNA damage sustained by the majority of cells in the body over the short course of the life of a progeria patient. This leaves me of two minds: 1), the DNA damage to the somatic cells of a patient would cause them to lose tissues more rapidly, which would have to be regenerated more quickly, causing more rapid degradation of tissues – shortening telomeres would take care of that. This could be cause a more rapid aging process. However, 2) the textbook just finished describing how stem cells and rapidly reproducing progenitor cells are dramatically more sensitive to DNA damage, which are the precursors involved in tissue repair. Wouldn’t it be more likely then that people suffering with this disease are actually drawing down their supply of stem cells more quickly than people without DNA repair defects? All of their tissues may also suffer more rapid degradation than normal, but it’s the stem cells which are clearly required for long term tissue maintenance. An interesting experiment could be done on these patients requiring no more than a few milliliters of blood – has their CD34+ ratio of cells dropped compared to non-sufferers of the disease? Alas, that’s well outside of what I can do in the next couple of years, so I hope someone else gives this a whirl.

Anyhow, just some random thoughs. 6 days left till the exam!


>It has been a VERY busy week since I last wrote. Mainly, that was due to my committee meeting on Friday, where I had to present my thesis proposal. I admit, there were a few things left hanging going into the presentation, but none of them will be hard to correct. As far as topics go for my comprehensive exams, it sounds like the majority of the work I need to do is to shore up my understanding of cancer. With a field that big, though, I have a lot of work to do.

Still, it was encouraging. There’s a very good chance I could be wrapping up my PhD in 18-24 months. (=

Things have also been busy at home – we’re still working on selling a condo in Vancouver, and had two showings and two open houses over the weekend, and considering the open houses were well attended,that is an encouraging sign.

FindPeaks has also had a busy weekend, even though I wasn’t doing any coding, myself. A system upgrade took FindPeaks off the web for a while and required a manual intervention to bring that back up. (Yay for the Systems Dept!) A bug was also found in all versions of 3.1 and 3.2, which could be fairly significant -and I’m still investigating. At this point, I’ve confirmed the bug, but haven’t had a chance to identify if it’s just for this one file, or for all files…

Several other findpeaks projects are also going to be coming to the forefront this week. Controls and automated file builds. Despite the bug I mentioned, FindPeaks would do well with an automated trunk build. More users would help me get more feedback, which would help me figure out what things people are using, so I can focus more on them. At least that’s the idea. It might also recruit more developers, which would be a good thing.

And, of course, several new things that have appeared that I would like to get going on: Bowtie is the first one. If it does multiple alignments (as it claims to), I’ll be giving it a whirl as the new basis of some of my work on transcriptomes. At a rough glance, the predicted 35x speedup compared to Maq is a nifty enticement for me. Then there’s the opportunity to do some clean up code on the whole Vancouver package for command line parameter processing. A little work there could unify and clean up several thousand lines of code, and make new development Much easier.

First things first, though, I need to figure out the source and the effects of that bug in findpeaks!