22 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…
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
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…
Martin Coleman
There is a multitude of licenses out there for a software developer to choose from, but a lot of programmers would prefer to not have to have a legal degree in order to understand them and would rather just have their code out in the public being used. This paper examines a few of the more popular and common software…
Yo Yehudi, Carole Goble, Caroline Jay
The global value of open source software is estimated to be in the billions or trillions worldwide 1 , but despite this, it is often under-resourced and subject to high-impact security vulnerabilities and stability failures 2,3 . In order to investigate factors contributing to open source community longevity, we…
João Pedro Moraes, Ivanilton Polato, Igor Wiese, Filipe Saraiva + 1 more
'Gustavo Pinto'] Abstract Open source licenses create a legal framework that plays a crucial role in the widespread adoption of open source projects. Without a license, any source code available on the internet could not be openly (re)distributed. Although recent studies provide evidence that most popular open source…
Madiha Zahrah Choksi, Ilan Mandel, David Goedicke, Yan Shvartzshnaider
'Yan Shvartzshnaider'] Centralization in code hosting and package management in the 2010s created fundamental shifts in the social arrangements of open source ecosystems. In a regime of centralized open source, platform effects can both empower and detract from communities depending on underlying technical…
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…
Muhammad Farooq‐i‐Azam
There is no denying the fact that with the widespread usage of computers and the Internet in our daily lives, security of information and data has gained increased attention. Information stored in electronic form is more susceptible to being leaked to unauthorized individuals intentionally or without intent. One of the…
Authors not listed
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high…
Murtaza Hussain Shaikh
According to different opponents and commercial giants in software industries, the open source style software development has enough capacity to complete successfully the large scale projects. But we have seen many flaws and loops in collaboration and handling of mega scale projects in open source environment. Perhaps…
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…
Authors not listed
Raman spectroscopy is an increasingly powerful and fast-growing analytical technique across diverse disciplines, from materials science and chemistry to biology and medicine, thanks to advances in Raman instrumentation and greatly supported by the flourishing of chemometrics and artificial intelligence (AI). However…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
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…
Authors not listed
The discoverability and reusability of data is critical for machine learning to drive new discovery in the chemical sciences, and the ‘FAIR Guiding Principles for scientific data management and stewardship’ provide a measurable set of guidelines that can be used to ensure the accessibility of reusable data. We…