I'm putting together a computational pipeline for a paper - a Makefile that runs a ton of stuff and outputs files, combined with an ipython notebook file that takes those output files and turns them into figures for inclusion in a LaTeX file. (Yes, very 2000, except for the ipython notebook …
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If you're like me, we pretend to care about the science in bioinformatics software. But what we really do is try to find reasons not to outright loathe the software -- because, lud knows, there are usually plenty of reasons to hate it.
In no particular order, here are the top …
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This blog post was inspired by two recent events.
First, in response to a NY Times article about the "data deluge" affecting biologists, one of my Facebook friends said something like "stop whining about how hard it is to analyze the data and do some good experiments instead!" I vehemently …
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First, I write a recipe file, 'metagenome.recipe', laying out my job description for, say, sequence trimming and assembly with Velvet:
fasta_file soil-data.fa qc_filter min_length=50 remove_Ns=true graph_filter min_length=400 velvet_assemble k=33 min_length=1000 scaffolding=True
Then I specify machine parameters, e.g. 'bigmem.conf':
[defaults] n_threads …read more
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If you've been under a rock (or indulging in arsenic yourself), you've heard about NASA's "arsenic" article, claiming the discovery of a microbial species that can substitute arsenate for phosphate. The paper was pre-announced via a press conference that then announced the results.
Immediate blogtastrophe! The paper was critically reviewed …
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I'm just finishing up my Computational Science for Evolutionary Biologists course, and I'm finding it tricky to come up with a good high-level summary of what I would like them to take away. As you can see from the class notes they've done some reasonably neat stuff with Digital Life …
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In thinking about open science and open communication about science, I've always been frustrated by the people who claim that the risks outweight the benefit. Their arguments seem sound if you buy into a certain kind of logic (the creationists will try to twist whatever you say! the climate change …
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