Bashing irreproducibility with shournal

Mapping Intimacies ◽

10.1101/2020.08.03.232843 ◽

2020 ◽

Author(s):

Tycho Kirchner ◽

Konstantin Riege ◽

Steve Hoffmann

Keyword(s):

Software Development ◽

Computer Science ◽

General Public ◽

Development Projects ◽

Entire Process ◽

Link Type ◽

Processing Steps ◽

General Public License

AbstractArguably, one of the most important tools for computer science is the Linux shell. Processing steps carried out there are critical for many analyses and software development projects. However, manual documentation of the work is time-consuming and error-prone. To remedy this problem, shournal tightly integrates with the shell and automatically records all shell commands along with associated file events. For any file, shournal allows the reconstruction of the command history and is able to create detailed reports for whole project directories. shournal is based on the fanotify API and mount namespaces and allows the efficient monitoring of entire process trees.AvailabilityThe code for shournal is freely available at https://github.com/tycho-kirchner/shournal under the GNU General Public License v3.0 or [email protected]

Download Full-text

dsSwissKnife: An R package for federated data analysis

10.1101/2020.11.17.386813 ◽

2020 ◽

Author(s):

Iulian Dragan ◽

Thomas Sparsø ◽

Dmitry Kuznetsov ◽

Roderick Slieker ◽

Mark Ibberson

Keyword(s):

Type 2 Diabetes ◽

Data Analysis ◽

General Public ◽

Biomarker Discovery ◽

R Package ◽

Link Type ◽

General Public License

ABSTRACTSummarydsSwissKnife is an R package that enables several powerful analyses to be performed on federated datasets. The package works alongside DataSHIELD and extends its functionality. We have developed and implemented dsSwissKnife in a large IMI project on type 2 diabetes, RHAPSODY, where data from 10 observational cohorts have been harmonised and federated in CDISC SDTM format and made available for biomarker discovery.Availability and implementationdsSwissKnife is freely available online at https://github.com/sib-swiss/dsSwissKnife. The package is distributed under the GNU General Public License version [email protected]

Download Full-text

A Fast and Memory-Efficient Implementation of the Transfer Bootstrap

10.1101/734848 ◽

2019 ◽

Cited By ~ 1

Author(s):

Sarah Lutteropp ◽

Alexey M. Kozlov ◽

Alexandros Stamatakis

Keyword(s):

General Public ◽

Efficient Implementation ◽

Random Tree ◽

Bootstrap Support ◽

Original Algorithm ◽

Link Type ◽

Branch Support ◽

General Public License ◽

Memory Efficient

AbstractRecently, Lemoine et al. suggested the Transfer Bootstrap Expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support metric on taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Therefore, we developed a fast and memory-efficient TBE implementation. We improved upon the original algorithm described by Lemoine et al. by introducing multiple algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× - 40× memory savings compared to booster. Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallelized version that also computes additional TBE-related statistics is available in pll-modules and RAxML-NG forks at: https://github.com/lutteropp/pll-modules/tree/tbe and https://github.com/lutteropp/raxml-ng/tree/tbe.

Download Full-text

Barriers Faced by Women in Software Development Projects

Information ◽

10.3390/info10100309 ◽

2019 ◽

Vol 10 (10) ◽

pp. 309

Author(s):

Edna Dias Canedo ◽

Heloise Acco Tives ◽

Madianita Bogo Marioti ◽

Fabiano Fagundes ◽

José Antonio Siqueira de Cerqueira

Keyword(s):

Software Development ◽

Computer Science ◽

Open Source ◽

Gender Equity ◽

Gender Bias ◽

Open Source Software ◽

Development Projects ◽

Software Projects ◽

Team Members ◽

Workplace Conditions

Computer science is a predominantly male field of study. Women face barriers while trying to insert themselves in the study of computer science. Those barriers extend to when women are exposed to the professional area of computer science. Despite decades of social fights for gender equity in Science, Technology, Engineering, and Mathematics (STEM) education and in computer science in general, few women participate in computer science, and some of the reasons include gender bias and lack of support for women when choosing a computer science career. Open source software development has been increasingly used by companies seeking the competitive advantages gained by team diversity. This diversification of the characteristics of team members includes, for example, the age of the participants, the level of experience, education and knowledge in the area, and their gender. In open source software projects women are underrepresented and a series of biases are involved in their participation. This paper conducts a systematic literature review with the objective of finding factors that could assist in increasing women’s interest in contributing to open source communities and software development projects. The main contributions of this paper are: (i) identification of factors that cause women’s lack of interest (engagement), (ii) possible solutions to increase the engagement of this public, (iii) to outline the profile of professional women who are participating in open source software projects and software development projects. The main findings of this research reveal that women are underrepresented in software development projects and in open source software projects. They represent less than 10% of the total developers and the main causes of this underrepresentation may be associated with their workplace conditions, which reflect male gender bias.

Download Full-text

The Evolution of Free Software

Handbook of Research on Open Source Software ◽

10.4018/978-1-59140-999-1.ch028 ◽

2011 ◽

pp. 363-372

Author(s):

Mathias Klang

Keyword(s):

Software Development ◽

Social Contract ◽

General Public ◽

Main Tool ◽

Free Software ◽

User Empowerment ◽

New Challenges ◽

The Many ◽

General Public License ◽

Free Software Foundation

The more we rely upon software to mediate the many facets of our lives the more important the ability to control and adapt that software to our needs becomes. The Free Software Foundation stands at the forefront for this effort to ensure user empowerment. The main tool of the foundation is the General Public License that has been a fundamental document in software development since its conception in 1989. At present the Free Software Foundation is in the process of launching a new version of their license and the process is similar to the development of an existing social contract—the delicate problem is meeting the new challenges that have appeared since the earlier version while maintaining the spirit of the original.

Download Full-text