Posts Tagged ‘i0afpsig’

Reference “Quantifying reproducibility in computational biolo…”

Friday, July 11th, 2014

PLoS ONE, 2013 vol. 8(11) pp. e80278

Quantifying reproducibility in computational biology: the case of the tuberculosis drugome.

Garijo, D; Kinnings, S; Xie, L; Xie, L; Zhang, Y; Bourne, PE; Gil, Y
How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to "reproducibility maps" that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. ….

.@pebourne Perhaps we need to educate biomedical data PhD students for more diverse careers #ismb #AFP14

The Second Machine Age: Work, Progress, and Prosperity in a Time of Brilliant Technologies:Amazon:Books

Friday, July 11th, 2014

mentioned in Bourne talk, might be a good read