The public package registry npm is one of the biggest software registry. With its 216 911 software packages, it forms a big network of software dependencies. In this paper we evaluate various methods for finding similar packages in the npm network, using only the structure of the graph. Namely, we want to find a way of categorizing similar packages, which would be useful for recommendation syst...

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale ...

We give a survey of the ParInt project for Parallel/ distributed Integration. We analyze the \generic" distributed adaptive integration algorithm and modify it to retain an eecient distribution of the global work load over the processors. With this goal we consider a distributed adaptive integration method based on a global heap priority queue, which remains load balanced and assures that the s...

SUMMARY We present a novel R package named synbreed to derive genome-based predictions from high-throughput genotyping and large-scale phenotyping data. The package contains a comprehensive collection of functions required to fit and cross-validate genomic prediction models. All functions are embedded within the framework of a single, unified data object. Thereby a versatile genomic prediction ...

We analyze the security properties of package management software. First, we examine many package managers for basic security properties and we perform an in-depth security audit for several chosen package managers. Next, we construct and demonstrate an automated end-to-end attack against CPAN, a popular packagemanager for Perl. Finally, we make recommendations on how to build more secure packa...

Mkpkg is a tool that helps software publishers create installation packages. Given software that is ready for distribution, mkpkg helps the publisher develop a description of the software package, including manifests, dependencies, and post-install customizations. Mkpkg automates many of the painstaking tasks required of the publisher, such as determining the complete package manifest and depen...

The GNU automatic software configuration tools, Autoconf, Automake, and Libtool, were designed to help the portability of software to multiple platforms. Such autotools also help improve the readability of code and speed up the development cycle of software packages. In this paper we quantify how helpful such autotools are to the open-source software development process. We study several large ...

We have developed a MatlabTMbased software package for bio-signal analysis. The software is based on modular design and can thus be easily adapted to fit on analysis of various kind of time variant or event-related bio-signals. Currently analysis programs for event-related potentials (ERP), heart-rate variability (HRV), galvanic skin responses (GSR) and quantitative EEG (qEEG) are implemented. ...

Background: It is assumed that the introduction of stochastic in mathematical model makes it more adequate. But there is virtually no methods of coordinated (depended on structure of the system) stochastic introduction into deterministic models. Authors have improved the method of stochastic models construction for the class of one-step processes and illustrated by models of population dynamics...