Principals, Practices, and Habits

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Some ideas I presented to a bioinformatics core about software development, literate programming, and versioning.

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  • Parameterize90% time futzing with figure graphics, legendsCloud computing design architectures
  • Principals, Practices, and Habits

    1. 1. Principles, Practices, and Habits<br />Jeremy Leipzig<br />December 18, 2010<br />
    2. 2. Gearing up for a data deluge<br />Technical<br />Scientific<br />Cultural<br />Version control<br />Documentation<br />Testing<br />Literate programming<br />
    3. 3. Principles, Practices, and Habits<br />
    4. 4. Results belong in reports, not emails<br />Answer a question once<br />Constant improvement<br />Associate results with a set of stated parameters<br />
    5. 5. Literate programming<br />Dynamic reports<br />Reproducible output<br />Marry code to reports<br />Marry data & configuration to reports<br />Reinforced sanity<br />
    6. 6. Sweave<br />R +<br />In R:<br />Sweave(“myReport.Rnw”,output=”myReport.tex”)<br />In shell:<br />echo "Sweave("myReport.Rnw",output="myReport.tex");" | R --no-save --quiet<br />In shell:<br />pdflatexmyReport.tex<br />chromosomeBias.Rnw sample:<br />svn co http://versioncontrol.chop.edu/svn/cbmi/chipSeq/trunk/chipSeqScripts<br />echo "configFile<-"bias.config.R";Sweave(”chromosomeBias.Rnw",output="chromosomeBias.tex");" | R --no-save --quiet<br />
    7. 7. bias.config.R<br />
    8. 8. Versioning<br />Subversion keyword substitution<br />svn add chromosomeBias.Rnw<br />svnpropsetsvn:keywords 'Revision' chromosomeBias.Rnw<br />svnci –m “added chromosomeBiassweave script”<br />$Rev$<br />http://svnbook.red-bean.com/en/1.5/svn.advanced.props.special.keywords.html<br />

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