Nozzle works with R 2.10 or later. Internally, reports are repre-sented as a
tree of report elements and implemented as nested R list objects. These lists
are rendered into HTML files that include a set of JavaScript functions to
support dynamic features of the user interface. For this purpose, JQuery
(

) are embedded, making Nozzle reports independent of
external library files. Likewise, Cascading Style Sheets (CSS) are embedded in the
HTML and used for layout and styling of the reports. The reports are compatible
with Firefox 4+, Chrome 12+, Safari 5+, Opera 11+ and Internet Explorer 9+.

We have deployed Nozzle in the context of the Firehose pipeline management 
system developed at the Broad Institute (

). 
Firehose is used for comprehensive automated and reproducible analyses of the 
data generated by The Cancer Genome Atlas (TCGA,

). 
In December 2012, the analysis workflow comprised approximately 35 different
modules. They cover a wide range of analyses on different data types, including
clustering of mRNA, miRNA and methylation data, copy number analysis with GISTIC
2.0

, mutation analysis, correlation analyses between
clinical and various molecular data, as well as pathway analyses. In this
project, a team of ten software developers and computational biologists from
four institutions (Broad Institute, Dana-Farber Cancer Institute, Harvard
Medical School, Institute for Systems Biology) used Nozzle to implement reports
for individual pipelines. The complete analysis workflow is currently run once
per month for each of 27 disease cohorts studied in TCGA, generating close to
500 reports. These reports are publicly available on the website of the TCGA
Genome Data Analysis Center (GDAC) at the Broad Institute (see above URL) and
archived by the TCGA Data Coordination Center. Between 1 February 2012 and 31
December 2012, more than 2,700 viewers have accessed over 17,000 reports in
approximately 6,000 visits.

We thank Dan DiCara, Lihua Zou, Douglas Voet and the members of the TCGA GDAC
at the Broad Institute for helpful comments.