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Iron Chef SynBio

I was reading a paper on brain refrigeration when Harry mentioned this experiment to me:

What was surprising was the dog was ischemic for 10 minutes! I would’ve thought brain swelling would’ve kicked in and prevented recirculation. This is fascinating.

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I was doing some next generation sequencing (NGS) analysis over the weekend, for the the first time. As such, I had to get some of the common software tools like PEAR and bowtie. Their official sites were hosted by SourceForge, but I didn’t want to download the binaries from SourceForge ’cause I’m paranoid about malware. So, I compiled them myself.

The process turned out to be super easy!

They all have git repos:

https://github.com/xflouris/PEAR

https://github.com/BenLangmead/bowtie

https://github.com/BenLangmead/bowtie2

For example, for bowtie, you can do:

git clone https://github.com/BenLangmead/bowtie.git
cd bowtie
make

For bowtie, you need libtbb, and for bowtie2, you need to compile with NO_TBB=1.

I’m pleasantly surprised because I remember the struggle of building open source projects when I was a young’un.

Just wanted to share!