Intro:

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Welcome to The Analytic Garden. I'll be using this site to write about technological issues that interest me. Some of it will be specific to students at Brown, some more general. I have another blog dealing with general issues, Before Completion, which is languishing from inattention.

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Julia and the Blockchain

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The blockchain cannot be described just as a revolution. It is a tsunami-like phenomenon, slowly advancing and gradually enveloping everything along its way by the force of its progression.   - William Mougayar I think the whole narrative of blockchain without bitcoin will amount to very little.  - Fred Ehrsam We want a language that’s open source, with a liberal license. We want the speed of C with the dynamism of Ruby. We want a language that’s homoiconic, with true macros like Lisp, but with obvious, familiar mathematical notation like Matlab. We want something as usable for general programming as Python, as easy for statistics as R, as natural for string processing as Perl, as powerful for linear algebra as Matlab, as good at gluing programs together as the shell. Something that is dirt simple to learn, yet keeps the most serious hackers happy. We want it interactive and we want it compiled. Why We Created Julia - Jeff Bezanson, Stefan Karpinski, Viral Shah, ...
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Filter Reads in Bam Files

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Recently, we wanted to remove low quality and duplicate reads from .bam alignment files to make viewing them in the UCSC genome browser easier. Our definition of low quality is stringent. We consider a read as low quality if it has any base with a base call quality below 30. To filter low quality reads and duplicates, we use a combination of samtools and the python PySam library. samtools has an option to remove PCR and optical duplicates and we use PySam to filter low quality reads. PySam allows us to read and write bam files. To filter out low quality reads, we loop through the input bam file, check the read quality to see if any base call falls below 30. If all of the base call qualities are 30 or above, we write the read to a new file. Here's one way to filter: def FilterReads(chrom, in_file, out_file):     def read_ok(read):         """         read_ok - reject reads with a low quality (be...
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School Shootings Are Political Violence

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It’s worth it to have a cost of, unfortunately, some gun deaths every single year so that we can have the Second Amendment to protect our other God given rights. ~ Charlie Kirk Charlie Kirk was killed on September 10, 2025. On the same day in Evergreen CO, two students were critically wounded during a shooting at school . Kirk's death resulted in politicians and pundits either declaring him a martyr or a victim of his own rhetoric.  Before September 10, I knew nothing about Charlie Kirk. From what I can gather since then, he shared views similar to those of many on the US right: contempt for LGBQ folks, trans people, black and brown people, and just about anyone not white, male, and christian. Flags were ordered to be flown at half-mast in honor of Kirk. The students shot in Colorado barely received thoughts and prayers . The news coverage of the Kirk shooting prompted me to look at shooting incidents, in particular school shootings. 2025 School Shootings in the USA I decided to l...
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