Related papers: pracpac: Practical R Packaging with Docker

Modern science clearly demands for a higher level of reproducibility and collaboration. To make research fully reproducible one has to take care of several aspects: research protocol description, data access, environment preservation,…

Reproducibility is a core requirement of modern scientific research. For computational research, reproducibility means that code should produce the same results, even when run on different systems. A standard approach to ensuring…

Container technologies such as Docker have become a crucial component of many software industry practices especially those pertaining to reproducibility and portability. The containerization philosophy has influenced the scientific…

A common problem in many disciplines is the need to assign a set of items into categories or classes with known labels. This is often done by one or more expert raters, or sometimes by an automated process. If these assignments or `ratings'…

In this paper, we present a new R package COREclust dedicated to the detection of representative variables in high dimensional spaces with a potentially limited number of observations. Variable sets detection is based on an original graph…

preCICE is a free/open-source coupling library. It enables creating partitioned multi-physics simulations by gluing together separate software packages. This paper summarizes the development efforts in preCICE of the past five years. During…

Discovering causal relationships from data is the ultimate goal of many research areas. Constraint based causal exploration algorithms, such as PC, FCI, RFCI, PC-simple, IDA and Joint-IDA have achieved significant progress and have many…

I present an R package called edibble that facilitates the design of experiments by encapsulating elements of the experiment in a series of composable functions. This package is an interpretation of "the grammar of experimental designs" by…

Here I present the freegroup package for working with the free group on a finite set of symbols. The package is vectorised; internally it uses an efficient matrix-based representation for free group objects but uses a configurable print…

Summary: R and Matlab are two high-level scientific programming languages which are frequently applied in computational biology. To extend the wide variety of available and approved implementations, we present the Rcall interface which runs…

We present a suite of Mathematica-based computer-algebra packages, termed "Kranc", which comprise a toolbox to convert (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code. Kranc can be used as a…

An R package SpatialPack that implements routines to compute point estimators and perform hypothesis testing of the spatial association between two stochastic sequences is introduced. These methods address the spatial association between…

Cox analysis is a common clinical data analysis technique to link valuable variables to clinical outcomes including dead and relapse. In the omics era, Cox model batch processing is a basic strategy for screening clinically relevant…

Docker is a containerization service that allows for convenient deployment of websites, databases, applications' APIs, and machine learning (ML) models with a few lines of code. Studies have recently explored the use of Docker for deploying…

Solving the software dependency issue under the HPC environment has always been a difficult task for both computing system administrators and application scientists. This work would like to tackle the issue by introducing the modern…

In this paper we introduce the software package ProPane, written for the R data analysis language. ProPane combines the full range of wcslib projections with the C++ image manipulation routines provided by the CImg library. ProPane offers…

Docker has gained attention as a lightweight container-based virtualization platform. The process for building a Docker image is defined in a text file called a Dockerfile. A Dockerfile can be considered as a kind of source code that…

Software repository mining is the foundation for many empirical software engineering studies. The collection and analysis of detailed data can be challenging, especially if data shall be shared to enable replicable research and open science…

Be it for a malicious or legitimate purpose, packing, a transformation that consists in applying various operations like compression or encryption to a binary file, i.e. for making reverse engineering harder or obfuscating code, is widely…

We describe preliminary investigations of using Docker for the deployment and testing of astronomy software. Docker is a relatively new containerisation technology that is developing rapidly and being adopted across a range of domains. It…