Professor Matthias Troyer (ETH Zurich) and his collaborators have published a number of papers whose results are fully reproducible. He is using VisTrails to both carry out the experiments and to package them for publication.
The journal Biostatistics has an associate editor for reproducibility who can assign grades of merit to conditionally accepted papers: D: data are available, C: code is available, and R: the AE could run the code and reproduce the results without much effort.
Linda B. Buck, who shared the 2004 Nobel Prize in Physiology or Medicine for deciphering the workings of the sense of smell, has retracted two scientific papers after she and her colleagues were unable to repeat the findings.
The code, data structures, experimental design and parameters, documentation, and figures are all important for scholarship communication and result replication. The author proposes the reproducible research standard for scientific researchers to use for all components of their scholarship that should encourage reproducible scientific investigation through attribution, facilitate greater collaboration, and promote engagement of the larger community in scientific learning and discovery.
Sweave is a tool that allows to embed the R code for complete data analyses in latex documents, and is automatically packaged in R installations. The purpose is to create dynamic reports, which can be updated automatically if data or analysis change. Instead of inserting a prefabricated graph or table into the report, the master document contains the R code necessary to obtain it. When run through R, all data analysis output (tables, graphs, etc.) is created on the fly and inserted into a final latex document. The report can be automatically updated if data or analysis change, which allows for truly reproducible research. It does not, however, track provenance.