Reproducible research concepts and tools for cancer bioinformatics

"Reproducible research" refers to a publishing discipline, originating in the geosciences, in which journal articles are accompanied by publication of data resources and software sufficient to allow independent reproduction of all tables and figures presented in articles. This paper reviews concepts of reproducible research in connection with cancer bioinformatics. The importance of reproducible discipline in the face of analytic complexity of microarray studies is documented with two case studies, and the role of portable self-documenting data and software archives in securing reproducibility is described. Legal protections for those engaged in reproducible research are discussed in the context of current US copyright law; a reproducible research standard that formalizes rights and obligations of those engaged in reproducible research is detailed. There is every indication that reproducible discipline is feasible for microarray studies, and reliability of inferences in cancer bioinformatics will be enhanced if commitments to concrete reproducibility are broadly accepted in the research community.