This is a course on Reproducible Research (RR) [1] for research engineers working with software applications in Pattern Recognition (PR) and Machine Learning (ML) [2]. It motivates and explains concepts behind RR, an increasing trend in scientific publications in this niche, its implications and tools for implementing it on an individual or group levels. It is a hands-on course in the sense stu...

One of the biggest problems in regression testing of a concurrent or distributed program is non-deterministic behavior which may produce diierent results from previous test with same test data. To solve this, we propose a set of synchronized-communication primitives and a new replay algorithm which uses these primitives to arrange all the execution sequences of non-deterministic operations. Com...

INTRODUCTION: Orthopaedic prostheses implantation is an invasive surgical procedure, with an increased risk for post-operative infections. Since the life span and quality of these implants is improving and more prostheses are implanted every year, the incidence of post-operative infections will increase. Most implants are based on titanium or nickel-chromemolybdenum alloys, while their overall ...

New tools for reproducible exploratory data analysis of large datasets are important to address the rising size and complexity of genomic data. We developed the valr R package to enable flexible and efficient genomic interval analysis. valr leverages new tools available in the "tidyverse", including dplyr. Benchmarks of valr show it performs similar to BEDtools and can be used for interactive a...

Letters to the Editor will be published, if suitable, as space permits. They should not exceed 1000 words (typed double-spaced) in length and may be subject to editing or abridgment. Rossi et al recently concluded that the aldosterone:renin ratio (ARR) is reproducible. 1 However, we think that several common errors were performed in their data interpretation, as described below. In the Bland-Al...

Research databases are an important building block in eScience and computational science investigations. For enabling reproducible research, an approach is needed which supports the identification and citation of the exact data (sub)sets utilized in experiments. While this itself is a challenge, in many cases the data stored in databases is sensitive and needs to be protected. Due to the increa...

There is a need for a method to facilitate the development of novel, reproducible colloidal surface-enhanced Raman scattering (SERS) substrates to encourage the use of SERS in applied studies. In this study we show for the first time that by using suitably designed SERS experiments in conjunction with multivariate analysis of variance (MANOVA), an objective assessment of colloidal SERS reproduc...

Numerical reproducibility failures appear in massively parallel floating-point computations. One way to guarantee the numerical reproducibility is to extend the IEEE-754 correct rounding to larger computing sequences, as for instance for the BLAS libraries. Is the overcost for numerical reproducibility acceptable in practice? We present solutions and experiments for the level 1 BLAS and we conc...

Knowing how scientific results are obtained, meaning to know which methods, techniques, algorithms, software etc. were used, is important for those scientific results to be credible. Documentation and provenance data provide exactly this information. However, providing documentation and provenance data is not trivial. In the domain of Modeling & Simulation a multitude of different building bloc...

In many applications, one is interested in determining which of the properties of a network module change across conditions. For example, to validate the existence of a module, it is desirable to show that it is reproducible (or preserved) in an independent test network. Here we study several types of network preservation statistics that do not require a module assignment in the test network. W...