The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have provided a strong basis for rapid development and deployment of innovative and flexible research software for scientific computation. A primary objective of this initiative is achievement of total remote reproducibility of novel algorithmic research results.
Bioinformatics | Computational Biology | Numerical Analysis and Computation
Gentleman, Robert C.; Carey, Vincent J. ; Bates, Douglas J.; Bolstad, Benjamin M.; Dettling, Marcel; Dudoit, Sandrine; Ellis, Byron; Gautier, Laurent; Ge, Yongchao; Gentry, Jeff; Hornik, Kurt; Hothorn, Torsten; Huber, Wolfgang; Iacus, Stefano; Irizarry, Rafael; Leisch, Friedrich ; Li, Cheng; Maechler, Martin; Rossini, Anthony J.; Sawitzki, Guenther; Smith, Colin; Smyth, Gordon K.; Tierney, Luke; Yang, Yee Hwa; and Zhang, Jianhua , "Bioconductor: Open software development for computational biology and bioinformatics" (January 2004). Bioconductor Project Working Papers. Working Paper 1.