1. My new data analysis pipeline code

    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':

    n_threads …
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  2. CSE 891, Computational Science for Evolutionary Biologists

    Course page at: http://ged.msu.edu/courses/2010-fall-cse-891/:

    This course will introduce biologists to computational thinking, practical computational techniques, and research topics in computational evolution. The course will consist of three intensive hands-on 5-week modules: computational competence in UNIX; data mining and hypothesis generation using the Avida digital life …
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