11 papers · ranked by Valyu relevance
Andrew Morin, Jennifer Urban, Piotr Sliz, Fran Lewitter
Source code is the human readable form of a computer programming language. “Open source” refers to licenses that require the source code be available to users, and that users be able to reuse, modify, and distribute the code . Without access to source code, researchers cannot effectively inspect, understand, or…
Mark Fingerhuth, Tomáš Babej, Peter Wittek, Leonie Anna Mueck
Open source software is becoming crucial in the design and testing of quantum algorithms. Many of the tools are backed by major commercial vendors with the goal to make it easier to develop quantum software: this mirrors how well-funded open machine learning frameworks enabled the development of complex models and…
Christine Årdal, Annette Alstadsæter, John-Arne Røttingen
Background Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for…
Rita Kukafka, Neil Chue Hong, Simon Hettrick, Ye Ye + 21 more
Background The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term…
Eric Deibel
The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to…
Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg + 11 more
A ‘Ten Simple Rules’ guide to git and GitHub. We describe and provide examples on how to use these software to track projects, as users, teams and organizations. We document collaborative development using branching and forking, interaction between collaborators using issues and continuous integration and automation…
Matthew H Todd
Scientific data are being generated and shared at ever-increasing rates. Two new mechanisms for doing this have developed: open access publishing and open source research. We discuss both, with recent examples, highlighting the differences between the two, and the strengths of both.
K. A. S. Mislan, Jeffrey M. Heer, Ethan P. White
Journals can promote the release of code used in ecological studies though a combination of increasing the visibility and discoverability of code and software and requiring code archiving. One way to increase visibility is to indicate code availability in the table of contents of all formats of the journal and have…
Dana E. Cobb-Lewis, Devin Synder, Sonya Dumanis, Robert Thibault + 6 more
The open science movement aims to transform the research landscape by promoting research transparency in order to enable reproducibility and replicability, lower the barriers for collaboration, and reduce unnecessary duplication. Recently, in recognition of the value of open science, funding agencies have begun to…
Nico Riedel, Miriam Kip, Evgeny Bobrov
Open research data are increasingly recognized as a quality indicator and an important resource to increase transparency, robustness and collaboration in science. However, no standardized way of reporting Open Data in publications exists, making it difficult to find shared datasets and assess the prevalence of Open…
Pamela H Russell, Rachel L Johnson, Shreyas Ananthan, Benjamin Harnke + 1 more
In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. The purpose of this paper is to investigate the…