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def science { }: Don't do this

http://defsci.blogspot.com/2013/06/dont-do-this.html

Bioinformatics on the cloud. Saturday, June 22, 2013. This past week I gave my boss and co-workers notice that I was moving on from UPENN. Normally you wouldn't do this sort of thing until you actually have an offer letter in hand. And for most people I would recommend the latter strategy. So why did I do it? The main reason is that I love the group I work for. Specifically Garret FitzGerald. You may be thinking to yourself right about now "if you love it so much, why are you leaving? So where to now?

defsci.blogspot.com

def science { }: August 2013

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Bioinformatics on the cloud. Sunday, August 4, 2013. Monday August 5th I start at Amazon Web Services as a Sr. Solutions Architect. While I have some idea of what the role entails, which is generally to help people use cloud computing for solving scientific and high-performance computing problems, I am under no illusion that I will know what it will actually be like in practice. Or what career paths just opened up for me. I am super excited and am bouncing-off-the-walls excited for tomorrow to come.

defsci.blogspot.com

def science { }: December 2007

http://defsci.blogspot.com/2007_12_01_archive.html

Bioinformatics on the cloud. Tuesday, December 11, 2007. Ask not for what you think you need. Yet, the town folk keep insisting "we need LIMS, please give.". LIMS are probably the only thing that potentially fits the bill for experimental data management, so that's what benchers ask for, when most likely a digital asset management application would suffice. Heck, even all those bit torrent sites can potentially do the job that researchers need. Are you in a regulated environment? Use of the LIMS? Promote...

defsci.blogspot.com

def science { }: January 2010

http://defsci.blogspot.com/2010_01_01_archive.html

Bioinformatics on the cloud. Friday, January 22, 2010. Ruby AWS = Easy Map-Reduce. As read lengths grow, we have found that the current crop of short read aligners don't seem to do very well with RNA-seq data. In a recent experiment we were only able to map about 40% of the reads using Bowtie. Was able to map an additional 45% percent of the reads, but was orders of magnitude slower than Bowtie (3 hours vs 8 days.). I decided to try out my hand at using Amazon Web Services. That script takes the public u...

defsci.blogspot.com

def science { }: Getting Promise Pegasus to actually email you in case of drive failure

http://defsci.blogspot.com/2012/01/getting-promise-pegasus-to-actually.html

Bioinformatics on the cloud. Wednesday, January 18, 2012. Getting Promise Pegasus to actually email you in case of drive failure. Has posted an excellent update to these scripts that take advantage of launchd to run these processes. See this gist. A nice feature of the system, though, is that the included Promise Utility GUI that ships with the array also installs quite a full featured command line utility. For instance, you can get a quick report of the drives in the array by issuing the following:.

defsci.blogspot.com

def science { }: February 2011

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Bioinformatics on the cloud. Monday, February 21, 2011. Compile BLAT on x86 64 Ubuntu 10.04. Recently I needed to compile BLAT for x86 64 on Ubuntu 10.04 server. The BLAT pre-compiled binaries for linux are 32-bit. Here is how you do it:. Remove the -Werror compiler flag to treat warnings as errors. Mkdir -p /bin/x86 6. Step (3) above requires editing the. File, line 17 goes from. HG WARN ERR = -DJK WARN -Wall -Werror. HG WARN ERR = -DJK WARN -Wall. Make places the executables into /bin/x86 64.

defsci.blogspot.com

def science { }: February 2008

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Bioinformatics on the cloud. Friday, February 15, 2008. Sequel's lackluster to *. Sequel is a great bare-bones ORM, but the bare-bones quality of Sequel: Model leave something to be desired. For instance the obj.to json method just calls the default ruby object inspect method, which prints out the class name and memory space. Not helpful. Also no to xml() for easy REST incorporation. Almost makes me want to go back to ActiveRecord, but then what's the point in using Merb? Merb TLS mail plugin gem. I took...

defsci.blogspot.com

def science { }: The new Mac Pro, Intel Phi, and the future of Bioinformatics

http://defsci.blogspot.com/2013/06/the-new-mac-pro-intel-phi-and-future-of.html

Bioinformatics on the cloud. Saturday, June 22, 2013. The new Mac Pro, Intel Phi, and the future of Bioinformatics. The other detriment to these sorts of algorithms was that most bioinformatitians tended to stick to interpreted languages such as Perl, Ruby and Python. The programmer productivity gains were tremendous and the languages are “fast enought”. For RNA-Seq alignment, show us the value of compiled languages paired with big RAM and big data pipes. In parallel to this, you have Continuum IO. It is...

defsci.blogspot.com

def science { }: October 2008

http://defsci.blogspot.com/2008_10_01_archive.html

Bioinformatics on the cloud. Tuesday, October 7, 2008. I've recently embarked on a study to see what effect clustering mass spectra has on the design of MRM experiments. Specifically one clusters spectra from the shotgun proteomics discovery phase of the experiment to see how it affects the selection of peptide species and the transitions that a mass spec looks for during the second targeted sequencing phase of the experiment. Blue = a decoy hit was scored in the clustered spectra, but not the original.

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def science { }: April 2008

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Bioinformatics on the cloud. Monday, April 14, 2008. Alternate title: "Bet Big, lose a long long time, then win so big that it makes your losses look like pocket change. Or maybe I'll just lose my shirt. Maybe both simultaneously, who knows? This post is motivated by a set of lectures I attended as part of the 3rd Annual ITMAT Symposium on Translational Medicine. Nassim Nicholas Taleb, PhD, London Business School, “Errors in the Analyses of Market Potential for Drugs”. Two days in ten years. Yikes. Or th...