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

1. Principles, Practices, and Habits Jeremy Leipzig December 18, 2010

2. Gearing up for a data deluge Technical Scientific Cultural Version control Documentation Testing Literate programming

3. Principles, Practices, and Habits

4. Results belong in reports, not emails Answer a question once Constant improvement Associate results with a set of stated parameters

5. Literate programming Dynamic reports Reproducible output Marry code to reports Marry data & configuration to reports Reinforced sanity

6. Sweave R + In R: Sweave(“myReport.Rnw”,output=”myReport.tex”) In shell: echo "Sweave(quot;myReport.Rnwquot;,output=quot;myReport.texquot;);" | R --no-save --quiet In shell: pdflatexmyReport.tex chromosomeBias.Rnw sample: svn co http://versioncontrol.chop.edu/svn/cbmi/chipSeq/trunk/chipSeqScripts echo "configFile<-quot;bias.config.Rquot;;Sweave(chromosomeBias.Rnwquot;,output=quot;chromosomeBias.texquot;);" | R --no-save --quiet

7. bias.config.R

8. Versioning Subversion keyword substitution svn add chromosomeBias.Rnw svnpropsetsvn:keywords 'Revision' chromosomeBias.Rnw svnci –m “added chromosomeBiassweave script” $Rev$ http://svnbook.red-bean.com/en/1.5/svn.advanced.props.special.keywords.html