Tation To provide to users the ability to fix bugs without waiting for the developer,

Tation To provide to users the ability to fix bugs without waiting for the developer, and to extend and improve the supplied software To encourage good scientific computing and statistical practice by exhibiting fully appropriate tools and instruction To provide a workbench of tools that allow researchers to explore and expand the methods used to analyze biological data To ensure that the international scientific community is the owner of the software tools needed to carry out research To lead and encourage commercial support and development of those tools that are successful To promote reproducible research by providing open and accessible tools with which to carry out that researchReproducible researchWe would like to address the reproducibility of published work in CBB. Reproducibility is important in its own right, and is the standard for scientific discovery. Reproducibility is an important step in the process of incremental improvement or refinement. In most areas of science researchers continually improve and extend the results of others but for scientific computation this is generally the exception rather than the rule. Buckheit and Donoho [35], referring to the work and philosophy of Claerbout, state the following principle: “An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete software development environment and that complete set of instructions that generated the figures.” There are substantial benefits that will come from enabling authors to publish not just an advertisement of their work but rather the work itself. A paradigm that fundamentally shifts publication of computational science from an advertisement of scholarship to the scholarship itself will be a welcome addition. Some of the concepts and tools that can be used in this regard are contained in [36,37]. When attempting to re-implement computational methodology from a published description many difficulties are encountered. Schwab et al. [38] make the following points: “Indeed the problem occurs wherever traditional methods of scientific publication are used to describe computational research. In a traditional article the author merely outlines the relevant computations: the limitations of a paper medium prohibit complete documentation including experimental data, parameter values and the author’s programs. Consequently, the PX-478 web reader has painfully to re-implement the author’s work before verifying and utilizing it…. The reader mustspend valuable time merely rediscovering minutiae, which the author was unable to communicate conveniently.” The development of a system capable of supporting the convenient creation and distribution of PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25636517 reproducible research in CBB is a massive undertaking. Nevertheless, the Bioconductor project has adopted practices and standards that assist in partial achievement of reproducible CBB. Publication of the data from which articles are derived is becoming the norm in CBB. This practice provides one of the components needed for reproducible research – access to the data. The other major component that is needed is access to the software and the explicit set of instructions or commands that were used to transform the data to provide the outputs on which the conclusions of the paper rest. In this regard publishing in CBB has been less successful. It is easy to identify major publications in the most prestigious jour.