In a play about Galileo, Bertold Brecht has one of his characters comment bitterly after Galileo's recantation that "unhappy is a land that breeds no heroes." The reply by Galileo is "unhappy is a land that needs heroes." This exchange was brought to mind by David Hartmann's comments [1] on Ralph Nader's call for whistle blowinc engineers. Hartmann points out the risks incurred by any engineer ...

N.B. The views expressed in this paper are those of the author(s) and do not necessarily correspond to the views of the European Central Bank. Hartmann of the European Central Bank. The usual caveat applies: The author is solely responsible for errors or omissions.

Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of...

The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at diffe...

Linear algebra operations are at the core of many Machine Learning (ML) programs. At the same time, a considerable amount of the effort for solving data analytics problems is spent in data preparation. As a result, end-toend ML pipelines often consist of (i) relational operators used for joining the input data, (ii) user defined functions used for feature extraction and vectorization, and (iii)...

MOTIVATION The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as port...

The Human Connectome Project (HCP) faces the challenging task of bringing multiple magnetic resonance imaging (MRI) modalities together in a common automated preprocessing framework across a large cohort of subjects. The MRI data acquired by the HCP differ in many ways from data acquired on conventional 3 Tesla scanners and often require newly developed preprocessing methods. We describe the mi...

Most existing HLT pipelines assume the input is pure text or, at most, HTML and either ignore (logical) document structure or remove it. We argue that identifying the structure of documents is essential in digital library and other types of applications, and show that it is relatively straightforward to extend existing pipelines to achieve ones in which the structure of a document is preserved.

Motivation: Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over distributed computer clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate...

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate...