>Update to blog url

>Just a quick admin note – I’m finally going to make the blog the default page on my domain, so for people who have this page bookmarked, you’ll want to drop the “blog.html” part of the URL.

As far as I can tell, people aren’t spending a lot of time looking at my photography, so I may as well let the blog tell the main story here.

Just in case you find yourself at the blog.html page, and aren’t sure where to go, just follow this link to fejes.ca

>Collection of all of the AGBT 2009 notes

>I’ve had several requests for a link to all of my notes from AGBT 2009, so – after some tweaking and relabeling – I’ve managed to come up with a single link to all of the AGBT postings. (There are a few very sparse postings from AGBT 2008, but they don’t contain much information that’s really useful.

Anyhow, if you’d like the link to all of my notes, you can find them here: http://www.fejes.ca/labels/AGBT%202009.html

>Time for a new look

>For people who read my blog on my web page, rather than through feeds, you might notice that my page looks different today. I had some feedback from other bloggers at AGBT (in particular, Daniel MacArthur of Genetic Future), who made some suggestions that should have been simple to implement. Unfortunately, my template is so customized, it’s nearly impossible to make the changes without breaking the layout.

So, I figured the best thing to do is clean up and start from scratch. If you notice odd changes in the template, that would be why. (=

In the meantime, there’s lots of good FindPeaks news – including controls, which are starting to work, new file formats, and a HUGE speed increase. (Whole genome runs in 6 minutes with a control… wow.)

Anyhow, I’ve got lots to do – and don’t mind the blog template tinkering, 6 minutes at a time.

>Site Feed changes

>I’m never one to shy away from changes, even when I should probably know better. One of the things that came up yesterday while talking to the other (read: much more professional) science bloggers was that I should be monitoring my rss feeds, and they all unanimously suggested feedburner.

Of course, I’ve never set it up before, so I’m still in the process of trying to figure out how it works – but hang in, I’ve still got another half hour before the first session starts. That should be more than enough time, right?

>It never rains, but it pours…

>Today is a stressful day. Not only do I need to to finish my thesis proposal revisions (which are not insignificant, because my committee wants me to focus more on the biology of cancer), but we’re also in the middle of real estate negotiations. Somehow, this is more than my brain can handle on the same day… At least we should know by 2pm if our counter-offer was accepted on the sales portion of the transaction, which would officially trigger the countdown on the purchase portion of the transaction. (Of course, if it’s not accepted, then more rounds of offers and counter-offers will probably take place this afternoon. WHEE!)

I’m just dreading the idea of doing my comps the same week as trying to arrange moving companies and insurance – and the million other things that need to be done if the real estate deal happens.

If anyone was wondering why my blog posts have dwindled down this past couple of weeks, well, now you know! If the deal does go through, you probably won’t hear much from me for the rest of this year. Some of the key dates this month:

  • Dec 1st: hand in completed and reviewed Thesis Proposal
  • Dec 5th: Sales portion of real estate deal completes.
  • Dec 6th: remove subjects on the purchase, and begin the process of arranging the move
  • Dec 7th: Significant Other goes to Hong Kong for~2 weeks!
  • Dec 12th: Comprehensive exam (9am sharp!)
  • Dec 13th: Start packing 2 houses like a madman!
  • Dec 22nd: Hannukah
  • Dec 24th: Christmas
  • Dec 29th: Completion date on the new house
  • Dec 30th: Moving day
  • Dec 31st: New Years!

And now that I’ve procrastinated by writing this, it’s time to get down to work. I seem to have stuff to do today.

>Two milestones reached

>Two of my three projects have met significant milestones this weekend, which I thought were worth sharing.

The first one is that FindPeaks had it’s first official patch submitted to me from developers outside the Genome Science Centre, on sunday night. Thank you very much to the submitters! I’m very glad to see someone using (and playing with!) the code. While the patch was minor, it tells me that there is definitely use in having released it to the wild.

The second milestone is for my blog, and while it’s not officially a “project” in the academic sense of the word, has consumed enough of my time that it starts to feel like one. The milestone? There are now as many people coming here directly as there are finding it through google. It’s not a huge number of hits, but it’s nice to know there’s an audience who’s enjoying my random rants. (-:

>Hello to Oregon State University.

>I love google analytics, but I always forget to look at it. It’s such a fantastic interface. Unfortunately, I can’t see the individual IP addresses of the people who are hitting my blog, but I can see the cities from which I’m getting traffic.

Can you believe nearly 1/2rd of my traffic comes from Corvallis, Oregon? Something like 25 hits a day. (Yes, I average around 50 hits a day on my blog.) So, what’s in Corvallis? The only thing I can find is the Oregon State University – which incidentally has a Center for Genome Research and Biocomputing, where they do some Illumina related Sequencing. Coincidence? Maybe.

Anyhow, I just thought I’d say hi to whoever it is in Corvallis that likes my blog. (=

>AGBT post #1.

>I’m here.. and online. I almost didn’t make it, thanks to bad weather in florida, but at least the car we rented didn’t break down on the road, the way the other group’s did. Apparently the police saved them from the aligators and wild pigs… No one can say AGBT hasn’t been exciting, so far.

Anyhow, lots of good topics, and meeting interesting people already. (I’m even sitting beside an exec from Illumina, in the ABI sponsored lunch.. how’s that for irony?) Anyhow, I’m excited to start the poster sessions and get some good discussions going.

Unfortunately, I missed two of the talks this morning, while I negotiated with the good people at United airlines to have my bag delivered. The three others I’ve seen so far have been good. Some interesting points:

The best graphics are the ones with the two DNA strands shown separately. Too cool – must include that in my FindPeaksToR scripts.

Loss or gain of homozygosity can screw up what you think you have, compared to what’s really there. Many models assume you have only one copy of a gene, or just don’t really do much to make sense of these events.

From David Cox, I learned that Barcoding isn’t new (it’s not), but that it usually doesn’t work well (I can’t prove that), but hey, they got it to work (and that’s good!).

And yes, my favorite line from David Cox’s presentation was something like: 900 PCR products, 90 people[‘s samples]… 1 tube. Make sure you don’t drop it!

Anyhow, I’m getting lots of ideas, and I’m thoroughly enjoying this conference. I’m saturated in next-gen sequencing work.

Anyhow, if anyone else is reading this, My poster is #38… feel free come come by and talk.

>Textbook Chapter

>Lately I haven’t had much to write about, as is clearly shown by the complete lack of content for the past month. I’ve been too busy to do much photography (I haven’t even put up my most recent shots onto my web page)… but I have figured out some of what I’d like my blog to be, and I’m going to put some effort into breaking it up into two sections: photography and Grad School.

Of course, that will have to wait until I come back from my trip – oh, right – I don’t think I mentioned I’ll be in England, Scotland and Wales for about 10 days. This trip has been in the works for two years, so you can imagine that I’ve been looking forward to it… just a little bit. (-;

Anyhow, before I go, I have a few things to finish, once of which is a textbook chapter. I agreed to take this project on about a month ago, and since it’s on an area in which I’m actively working, I thought it would be a good idea.

The topic of the chapter is a method or protocol called ChIP-Seq (or ChIPSeq, or ChIP-Solexa, or a few other things, actually), which is a combination of chromatin immunoprocipitation and a so-called “next-generation” sequencing technology. (If anyone wants to know more, send me a message, and I’ll do a post on it.)

At any rate, when I was first approached about it, I was in the process of rewriting all of the production code that’s being used to analyze the results – so I’m now intimately familiar with how that works. And, once that was done, I spent the next week doing a scholarship application, for which I had to do some lit review.. and finally this week, I got to working on the chapter.
I spent a few days reading, a day outlining, and a few hours here and there doing some writing. It’s slow work, to be honest, but it’s getting there.

The funny part is that I found a great paper yesterday, that would have pointed me to the right place, and has a great introduction. Where did I find it, you ask? On my desk. I’ve had it for about 2 months – it’s the paper on ChIP-Seq written by the guy who sits across the cubicle wall from me.

Anyhow, That’s life. Now I just need to sit down and write like mad – I’d like to get a draft out before my vacation starts.

>One more “little” change..

>Alright – one more change. I’ve just moved to the “new blogger” from the old one (where I’ve been since 2001-ish). I wish I could say that I have a good reason for it, but it’s midnight, I’m addicted to bleeding-edge packages and I’ve already broken apache on my home computer. Doesn’t that scream that this is the perfect time to try an upgrade that I don’t need?

If you said no, you have way more common sense than I do. Else, I’m just itching to press the “publish” button, and see what this does to my web page! Lets go!